Gene correction of SCID-related genes in hematopoietic stem and progenitor cells

ABSTRACT

The present disclosure is in the field of genome engineering, particularly targeted integration of a functional SCID-related genes (e.g., IL2RG, RAG1 and/or RAG2 gene) into the genome of a cell for provision of proteins lacking or deficient in SCID.

CROSS-REFERENCE TO RELATED APPLICATIONS

The present application claims the benefit of U.S. ProvisionalApplication No. 62/030,942, filed Jul. 30, 2014, the disclosure of whichis hereby incorporated by reference in its entirety.

SEQUENCE LISTING

The instant application contains a Sequence Listing which has beensubmitted electronically in ASCII format and is hereby incorporated byreference in its entirety. Said ASCII copy, created on Aug. 31, 2015, isnamed 83250124SL.txt and is 23,191 bytes in size.

TECHNICAL FIELD

The present disclosure is in the field of genome engineering,particularly targeted modification of the genome of a cell, includingtargeted integration of a corrective transgene of a mutant SCID-relatedgene (e.g., IL2R-gamma (IL2RG) and/or recombination activating genes(RAG genes such as RAG1, RAG2)).

BACKGROUND

Recombinant transcription factors comprising the DNA binding domainsfrom zinc finger proteins (“ZFPs”) or TAL-effector domains (“TALEs”) andengineered nucleases including zinc finger nucleases (“ZFNs”), TALENs,CRISPR/Cas nuclease systems, and homing endonucleases that are alldesigned to specifically bind to target DNA sites have the ability toregulate gene expression of endogenous genes and are useful in genomeengineering and gene therapy. See, e.g., U.S. Pat. Nos. 9,045,763;9,005,973; 8,956,828; 8,945,868; 8,586,526; 8,329,986; 8,399,218;6,534,261; 6,599,692; 6,503,717; 6,689,558; 7,067,317; 7,262,054;7,888,121; 7,972,854; 7,914,796; 7,951,925; 8,110,379; 8,409,861; U.S.Patent Publications 20030232410; 20050208489; 20050026157; 20050064474;20060063231; 20080159996; 20100218264; 20120017290; 20110265198;20130137104; 20130122591; 20130177983 and 20130177960 and 20150056705,the disclosures of which are incorporated by reference in theirentireties for all purposes. Further, targeted nucleases are beingdeveloped based on the Argonaute system (e.g., from T. thermophilus,known as ‘TtAgo’, see Swarts et at (2014) Nature 507(7491): 258-261),which also may have the potential for uses in genome editing and genetherapy.

Nuclease-mediated gene therapy can be used to genetically engineer acell to have one or more inactivated genes and/or to cause that cell toexpress a product not previously being produced in that cell (e.g., viatransgene insertion and/or via correction of an endogenous sequence).Examples of uses of transgene insertion include the insertion of one ormore genes encoding one or more novel therapeutic proteins, insertion ofa coding sequence encoding a protein that is lacking in the cell or inthe individual, insertion of a wild-type gene in a cell containing amutated gene sequence, and/or insertion of a sequence that encodes astructural nucleic acid such as shRNA or siRNA. Examples of usefulapplications of ‘correction’ of an endogenous gene sequence includealterations of disease-associated gene mutations, alterations insequences encoding splice sites, alterations in regulatory sequences andtargeted alterations of sequences encoding structural characteristics ofa protein. Transgene construct(s) is(are) inserted by either homologydirected repair (HDR) or by end capture during non-homologous endjoining (NHEJ) driven processes. See, e.g., U.S. Pat. Nos. 9,045,763;9,005,973; 7,888,121 and 8,703,489.

Clinical trials using these engineered transcription factors andnucleases have shown that these molecules are capable of treatingvarious conditions, including cancers, HIV and/or blood disorders (suchas hemoglobinopathies and/or hemophilias). See, e.g., Yu et al. (2006)FASEB J. 20:479-481; Tebas et at (2014) New Eng J Med 370(10):901. Thus,these approaches can be used for the treatment of diseases.

Severe combined immunodeficiency (SCID) is a heterogeneous group ofprimary immunodeficiencies comprising at least 11 different conditions(Kutukeuler et al (2012) It J of Ped 38:8). All patients with SCID aresusceptible to infections from common bacteria and viruses as well asopportunistic and fungal pathogens. X-linked severe combinedimmunodeficiency (X-SCID) is an immunodeficiency disorder in which thebody produces very few T cells and natural killer cells. In the absenceof T cell help, B cells become defective (Fisher et al. (2002) NatureReviews 2:615-621). It is an X-linked recessive trait such that nearlyall patients are male, and stems from a mutated version of the IL2RGgene (also referred to as the “common gamma” gene or “common cytokinereceptor gamma chain”), located at xq13.1 on the X-chromosome. Thecommon gamma protein is shared between receptors for IL-2, IL-4, IL-7,IL-9, IL-15 and IL-21, leaving X-SCID patients unable to developfunctional T and NK cells. Persons afflicted with X-SCID often haveinfections very early in life, before three months of age. This occursdue to the decreased amount of immunoglobulin G (IgG) levels in theinfant during the three-month stage. This is followed by viralinfections such as pneumonitis, an inflammation of the lung whichproduces common symptoms such as cough, fever, chills, and shortness ofbreath. Recurrent eczema-like rashes are also a common symptom. Othercommon infections experienced by individuals with X-SCID includediarrhea, sepsis, and otitis media. Some other common symptoms that areexperienced by X-SCID patients include failure to thrive, gut problems,skin problems, and muscle hypotonia (Vickers Severe combined ImmuneDeficiency: Early Hospitalisation and Isolation (2009) pp. 29-47. ISBN978-0-470-31986-4). Without therapeutic and/or environmentalintervention, X-SCID is typically fatal during the first year of life(Hacein-Bey-Abina et al, (2002) NEJM 346: 1185-1193).

Another type of SCID is related to defects in the recombinationactivating genes (RAG1, RAG2), where approximately 10% of all SCID casesare tied to RAG1 or RAG2 (Ketukculer, ibid). The protein products of theRAG1 and RAG2 genes (Rag1 and Rag2, respectively) are essential forV(D)J rearrangement in B and T cell receptors, and thus are required forproper development of B cells and T cells and are also thought to beinvolved in inflammation (see, e.g., U.S. Patent Publication No.20110016543). Together, Rag1 and Rag2 initiate V(D)J recombination bycleaving DNA to generate double strand breaks which are then repaired bythe NHEJ machinery.

Omenn Syndrome is an autosomal recessive variant of SCID withdistinctive clinical features of generalized erythodermia,hepatosplenomegaly and lymphadenopathy. Unlike patients with classicSCID, patients with Omenn Syndrome have circulating T cells with anabnormal phenotype: they are typically poorly reactive, oligoclonal, anddisplay cell-surface markers of previous activation. B cells aretypically absent or low and IgG levels are generally low while IgElevels are high (Matthews et al (2015) PLoS One 10(4):e0121489). OmennSyndrome is typically caused by mutations in RAG1 or RAG2 althoughmutations in other genes can also lead to it. Generally, hypomorphic RAGmutations, sometimes in combination with RAG null mutations, lead toOmenn Syndrome (Matthews, ibid).

Currently, there are three types of treatments available for SCIDpatients, namely, the use of medication, sterile environments, andintravenous immunoglobulin therapy (IVIG). First, antibiotics orantivirals are administered to control opportunistic infections, such asfluconazole for candidiasis, and acyclovir to prevent herpes virusinfection (Freeman et al. Current Opinion in Allergy and ClinicalImmunology (2009) 9 (6):525-530). In addition, the patient can alsoundergo intravenous immunoglobulin (IVIG) supplementation. However, theIVIG is expensive, in terms of both time and money. In addition, theaforementioned treatments only serve to prevent opportunisticinfections, and are by no means a cure for X-SCID or other SCIDdisorders.

At present, bone marrow transplantation (BMT) is the standard curativeprocedure and results in a full immune reconstitution, if an appropriatedonor can be identified and if the engraftment is successful. A bonemarrow transplant requires an acceptable human leukocyte antigen (HLA)match between the donor and the recipient. As the array of HLA moleculesis different between individuals, cells of the immune system can utilizethe HLA apparatus to distinguish self from foreign cells. A BMT can beallogeneic (donor and recipient are different people) or autologous(donor and recipient are the same person). An autologous BMT thereforehas a full HLA match, whereas, a match for an allogenic BMT is morecomplicated. In standard practice, an allogenic graft is better when all6 of the known major HLA antigens are the same—a 6 out of 6 match.Patients with a 6/6 match have a lower chance of graft-versus-hostdisease, graft rejection, having a weak immune system, and gettingserious infections. For bone marrow and peripheral blood stem celltransplants, sometimes a donor with a single mismatched antigen isused—a 5 out of 6 match. Therefore, a BMT may result in a full immunereconstitution and thus be curative in an X-SCID patient, but potentialcomplications limit efficacy and widespread use. For patients with OmennSyndrome, BMT is also the preferred method of treatment however OmennSyndrome patients have a higher rate of mortality following BMT thanother SCID patients.

Previous gene therapy clinical trials for X-SCID patients have usedretroviral vectors comprising a wild type IL2RG gene (Cavazzana-Calvo etal. (2000) Science 288(5466):669-72). Retroviral vectors randomlyintegrate into the host genome, however, and thus can cause insertionaloncogenesis in patients when integration occurs in proto-oncogenes(Hacein-Bey-Abina et al. (2008) J. Clin Investigation 118(9):3132-42).The majority of patients undergoing this therapy developed leukemia as aresult of this insertional oncogenesis, thus this method is not a safeand effective therapy.

The development of integrase-deficient lentiviral vectors (IDLV)(Philippe et al. (2006) Proc. Nat'l Acad. Sci. 103(47):17684-9), orIDLV, has facilitated further investigation of gene correction of IL2RGfor X-SCID due to its inability to integrate into the host genome. Theability of zinc finger nucleases (ZFNs), transcription activator-likeeffector nucleases (TALENs), CRISPR/Cas systems and TtAgo to target aspecific region of DNA, introduce a targeted double stranded break,which then facilitates targeted integration of an introduced transgenemakes this genome editing technology highly attractive in thedevelopment of a potential curative treatment.

To this end, investigators have targeted exon 5 of the endogenous IL2RGlocus for ZFN cleavage and subsequent TI of IDLV-delivered correctiveIL2RG cDNA in hematopoietic stem and progenitor cells (HSPCs). See,e.g., U.S. Pat. Nos. 7,888,121 and 7,951,925; Lombardo et al. (2007) NatBiotech 25(11):1298-306; Genovese et al. (2014) Nature 510(7504):235-40.However, these methods may have potential disadvantages in thatintroducing a transgene in the middle of an exon creates a partiallytranscribed region upstream of the introduced transgene, which mayinterfere with the activity of the introduced corrective gene.Furthermore, the delivered episomal transgene may still be able torandomly integrate into the genome if another viral integrase is presentin the cell. Immunosuppressed patients (such as all X-SCID patients are)might have activation of endogenous retroviruses, thus barring patientswho are also HIV positive from receiving virally delivered gene therapyfor X-SCID treatment.

Thus, there remains a need for additional strategies of IL2RG and RAGgene correction and transgene donor delivery for treatment and/orprevention of SCID.

SUMMARY

The present invention describes compositions and methods for use in genetherapy and genome engineering. Specifically, the methods andcompositions described relate to targeted insertion of a transgene(donor) including protein-encoding sequence, for example a protein thatis lacking or deficient in a subject with a SCID. In certainembodiments, targeted integration of corrective SCID-related genecassette (e.g., IL2RG and/or RAG (RAG1 and/or RAG2)) into the genome ofa cell (e.g., hematopoietic stem cell with mutant versions of theSCID-related gene) using highly specific DNA binding proteins (ZFNs,TALENs, CRISPR/Cas systems). The SCID-related gene cassettes (e.g.,functional IL2RG and/or a RAG transgene) integrated into the targetedgene (e.g., IL2RG, RAG1, RAG2, HPRT, etc.) may be carried on a viral ornon-viral vector (e.g., adeno-associated viral (AAV)) and/or may beintegrated using one or more nucleases.

In one aspect, described herein is a zinc-finger protein (ZFP) thatbinds to target site in an IL2RG or RAG gene in a genome, wherein theZFP comprises one or more engineered zinc-finger binding domains. In oneembodiment, the ZFPs are a pair of zinc-finger nucleases (ZFNs) thatdimerize and then cleave a target genomic region of interest, whereinthe ZFNs comprise one or more engineered zinc-finger binding domains anda nuclease cleavage domain or cleavage half-domain. In another aspect,described herein is a TALE protein (Transcription activator likeeffector) that binds to target site in an IL2RG or RAG gene in a genome,wherein the TALE comprises one or more engineered TALE DNA bindingdomains. In one embodiment, the TALE is a nuclease (TALEN) that cleavesa target genomic region of interest, wherein the TALEN comprises one ormore engineered TALE DNA binding domains and a nuclease cleavage domainor cleavage half-domain. Cleavage domains and cleavage half domains ofZFNs and/or TALENs can be obtained, for example, from variousrestriction endonucleases and/or homing endonucleases. In oneembodiment, the cleavage half-domains are derived from a Type IISrestriction endonuclease (e.g., Fok I). In certain embodiments, the zincfinger or TALE DNA binding domain recognizes a target site in an IL2RGor RAG gene, for example in intron 1. In certain embodiments, the targetsite is as shown in Tables 2 or 4. In certain embodiments the ZFNcomprises a zinc finger protein having the recognition helix regions ofthe order as shown in Table 1. In other embodiments, the TALEN comprisesa TALE protein having the RVDs shown in Table 3. In still furtherembodiments, a CRISPR/Cas nuclease system that targets an IL2RG or RAGgene is described, for example a CRISPR/Cas nuclease system comprising aguide RNA that associates with a nuclease (cleavage) domain to form anactive nuclease. In certain embodiments, the guide RNA of the CRISPR/Cassystem is shown in Table 5. In still further embodiments, a TtAgo systemis used to effect cleavage. In preferred certain embodiments, thenuclease targets an intron (e.g., intron 1 or 2) of an IL2RG gene of aRAG gene. In other preferred certain embodiments, the nuclease targetsintron 2 of a RAG gene (e.g., RAG1 or a RAG2 gene). In especiallypreferred embodiments, the nuclease targets the IL2RG2 gene withinintron 1 and the RAG1 gene at chromosome 11, at position36,590,551-36,590,578 and 36,590,581-36,590,607 (site 1) or36,594,301-36,594,328 and 36,594,330-36,594,357 (site 4, where numbersare relative to UCSC GRCh37/hg19 human genome assembly.

The nuclease may bind to and/or cleave an IL2RG or RAG gene within thecoding region of the gene or in a non-coding sequence within or adjacentto the gene, such as, for example, a leader sequence, trailer sequenceor intron, or within a non-transcribed region, either upstream ordownstream of the coding region.

In another aspect, described herein are compositions comprising one ormore of the nucleases (ZFNs, TALENs, TtAgo and/or CRISPR/Cas systems)described herein, including a nuclease comprising a DNA-binding molecule(e.g., ZFP, TALE, sgRNA, etc.) and a nuclease (cleavage) domain. Incertain embodiments, the composition comprises one or more nucleases incombination with a pharmaceutically acceptable excipient. In someembodiments, the composition comprises two or more sets (pairs) ofnucleases, each set with different specificities. In other aspects, thecomposition comprises different types of nucleases. In some embodiments,the composition comprises polynucleotides encoding IL2RG-, RAG-specificnucleases, while in other embodiments, the composition comprises IL2RG-,RAG-specific nuclease proteins. In still further embodiments, thecomposition comprises one or more donor molecules, for example donorsthat encode a functional IL2RG, Rag1 and/or Rag2 protein(s), includingany functional fragment thereof. In preferred embodiments, the donorcomprises a partial IL2RG and/or RAG (e.g., RAG1 or RAG2) gene. Alsopreferred is a donor comprising a cDNA comprising exons 2 through 8 ofthe wild type IL2RG gene. Another preferred donor is a cDNA comprisingexon 3 of a wild type RAG (RAG1 and/or RAG2) gene.

In another aspect, described herein is a polynucleotide encoding one ormore nucleases or nuclease components (e.g., ZFNs, TALENs, TtAgo ornuclease domains of the CRISPR/Cas system) described herein. Thepolynucleotide may be, for example, mRNA or DNA. In some aspects, themRNA may be chemically modified (See e.g. Kormann et al, (2011) NatureBiotechnology 29(2):154-157). In other aspects, the mRNA may comprise anARCA cap (see U.S. Pat. Nos. 7,074,596 and 8,153,773). In furtherembodiments, the mRNA may comprise a mixture of unmodified and modifiednucleotides (see U.S. Patent Publication 2012-0195936). In anotheraspect, described herein is a nuclease expression vector comprising apolynucleotide, encoding one or more ZFNs, TALENs, TtAgo or CRISPR/Cassystems described herein, operably linked to a promoter. In oneembodiment, the expression vector is a viral vector, for example an AAVvector.

In another aspect, described herein is a host cell comprising one ormore nucleases and/or nuclease expression vectors. In certainembodiments, the host cell includes a mutant version of one or moreSCID-related genes (e.g., IL2RG and/or RAG gene) such that integrationof the SCID-related gene cassette provides a functional version of theprotein lacking or deficient in the cell. The host cell may be stablytransformed or transiently transfected or a combination thereof with oneor more nuclease expression vectors. In one embodiment, the host cell isa hematopoietic stem cell. In other embodiments, the one or morenuclease expression vectors express one or more nucleases in the hostcell. In another embodiment, the host cell may further comprise anexogenous polynucleotide donor sequence (e.g., encoding an IL2RG or Ragprotein). In any of the embodiments, described herein, the host cell cancomprise an embryo cell, for example a one or more mouse, rat, rabbit orother mammal cell embryo (e.g., a non-human primate). In someembodiments, the host cell comprises a tissue. Also described are cellsor cell lines descended from the cells described herein, includingpluripotent, totipotent, multipotent or differentiated cells comprisinga modification (e.g., integrated donor sequence) in an intron of anendogenous IL2RG and/or RAG gene (e.g., intron 1 of an endogenous IL2RG,or in intron 2 of an endogenous RAG1 or RAG2 gene). In certainembodiments, described herein are differentiated cells as describedherein comprising a modification (e.g., integrated donor sequence) in anintron of an endogenous IL2RG and/or RAG gene (e.g., intron 1 of anendogenous IL2RG, or in intron 2 of an endogenous RAG1 or RAG2 gene),which differentiated cells are descended from a stem cell as describedherein.

In another aspect, described herein is a method for cleaving an IL2RGand/or RAG gene in a cell, the method comprising: (a) introducing, intothe cell, one or more polynucleotides encoding one or more nucleasesthat target one or more IL2RG and/or RAG (RAG1 or RAG2) genes underconditions such that the nuclease(s) is(are) expressed and the one ormore IL2RG and/or RAG (RAG1 or RAG2) genes are cleaved.

In other embodiments, a genomic sequence in the target IL2RG and/or RAG(RAG1 or RAG2) gene is cleaved, for example using a nuclease (or vectorencoding the nuclease) as described herein and a “donor” sequenceinserted into the gene following targeted cleavage with the ZFN, TALEN,TtAgo or CRISPR/Cas system such that the donor sequence is expressed inthe cell. The donor sequence may encode a functional IL2RG or Ragprotein. In some embodiments, the donor sequence comprises a partialIL2RG and/or RAG (RAG1 or RAG2) gene sequence. In preferred embodiments,the donor comprises a partial cDNA of the IL2RG gene sequence comprisingexons 2 through 8, or a full cDNA of the RAG1 gene comprising exon 3, ora full cDNA of the RAG2 gene comprising exon 3. Furthermore, the donorsequence may be present in the nuclease delivery system (e.g., non-viralvector or viral vector), present in a separate delivery mechanism (e.g.,nuclease delivered in mRNA form and donor delivered using viral vectorsuch as AAV) or, alternatively, may be introduced into the cell using aseparate and/or different nucleic acid delivery mechanism. Insertion ofa donor nucleotide sequence into the IL2RG and/or RAG (RAG1 or RAG2)locus can result in the expression of the transgene under control of theendogenous IL2RG and/or RAG (RAG1 or RAG2) genetic control elements,respectively. In some aspects, insertion of the transgene of interestresults in expression of an intact exogenous protein sequence and lacksany IL2RG and/or RAG (RAG1 or RAG2)-encoded amino acids. In otheraspects, the expressed exogenous protein is a fusion protein andcomprises amino acids encoded by the transgene and by the IL2RG and/orRAG (RAG1 or RAG2) gene. In some instances, the IL2RG and/or RAG (RAG1or RAG2) sequences will be present on the amino (N)-terminal portion ofthe exogenous protein, while in others, the IL2RG and/or RAG (RAG1 orRAG2) sequences will be present on the carboxy (C)-terminal portion ofthe exogenous protein. In other instances, IL2RG and/or RAG (RAG1 orRAG2) sequences will be present on both the N- and C-terminal portionsof the exogenous protein.

In some embodiments, the invention describes methods and compositionsthat can be used to express a transgene under the control of the IL2RGand/or RAG (RAG1 or RAG2) promoter in vivo. In some aspects, thetransgene may encode a therapeutic protein of interest. The transgenemay encode a protein such that the methods of the invention can be usedfor protein replacement. In some aspects, the transgene encodes an IL2RGor Rag (e.g., Rag1 or Rag2) protein that treats and/or prevents SCID orOmenn Syndrome. In other aspects, the transgene comprises a partialIL2RG and/or RAG (RAG1 or RAG2), gene sequence.

In some embodiments, the nuclease target and/or cleavage site is in anintron of the IL2RG and/or RAG (RAG1 or RAG2) gene such that a transgene(e.g., IL2RG-, Rag1 or Rag2-encoding transgene) is integrated into anintronic region of IL2RG and/or RAG (RAG1 or RAG2), for example intointron 1, intron 2 or intron 2, respectively. The transgene may be underthe control of another endogenous or exogenous promoter of interest invivo or in vitro, which exogenous promoter drives expression of thetransgene (e.g., IL2RG-, Rag-encoding sequence). In preferredembodiments, the IL2RG, RAG1 or RAG2 transgene comprises a cDNAcomprising exons 2 through 8 of IL2RG, exon 3 of RAG1, or exon 3 ofRAG2, and further comprises a splice acceptor site such that uponintegration and expression, the endogenous IL2RG exon 1, the endogenousRAG1 exon 1 or 2 or the endogenous RAG2 exon 1 or 2 sequences are linkedto the transgenic exons 2-8 sequences, exon 3, or exon 3, respectively(depending on the RAG isoform) such that a wild type IL2RG, or Ragprotein is produced and treats or prevents X-SCID or Omenn Syndrome.

In another aspect, a method of modifying an endogenous gene isdescribed, the method comprising administering to the cell one or morepolynucleotides encoding one or more nucleases (e.g., ZFNs, TALENs,TtAgo, CRISPR/Cas system) in the presence of one or more donor sequenceencoding an IL2RG or Rag protein, such that the donor is integrated intothe endogenous gene targeted by the nuclease. Integration of one or moredonor molecule(s) occurs via homology-directed repair (HDR) or bynon-homologous end joining (NHEJ) associated repair. In certainembodiments, one or more pairs of nucleases are employed, whichnucleases may be encoded by the same or different nucleic acids. Anyendogenous gene can be targeted for nuclease-mediated targetedintegration of an IL2RG and/or RAG (RAG1 or RAG2) donor, including butnot limited to IL2RG (e.g., intron 1), RAG1 (e.g. intron 1 or 2), RAG2(e.g. intron 1 or 2), respectively, or a safe-harbor gene such as CCR5,AAVS1, Rosa26, ALB and/or HPRT.

In yet another aspect, provided herein is a cell comprising an IL2RG,RAG1 and/or RAG2 transgene which has been integrated into the genome ina targeted manner using a nuclease. In certain embodiments, the cell ismade by the methods described herein. In other preferred embodiments,the IL2RG, RAG1 or RAG2 transgene is integrated into an intronic regionof IL2RG (e.g., intron 1, including but not limited into a sequence asshown in any of SEQ ID NOs:47 to 60), RAG1 (e.g., intron 1 or 2,including but not limited into a sequences as shown as in any of SEQ IDNos:81 to 83) or RAG2 (e.g., intron 1 or 2). In other embodiments, theIL2RG and/or RAG (RAG1 or RAG2) transgene is integrated into asafe-harbor locus, such as CCR5, AAVS1, ALB, Rosa26 and/or HPRT. Thecells comprising the integrated IL2RG, and/or RAG (RAG1 or RAG2)transgene may express the transgene from an endogenous promoter (e.g.,the IL2RG, RAG1 or RAG2 promoter, respectively) or, alternatively, thetransgene may include regulatory and control elements such as exogenouspromoters that drive expression of the IL2RG, RAG1 or RAG2 transgene(e.g., when integrated into a safe harbor locus). In certainembodiments, the cells comprising an IL2RG transgene do not include anyviral vector sequences integrated into the genome.

In any of the methods and compositions described herein, the cells maybe any eukaryotic cell. In certain embodiments, the cells arepatient-derived, for example autologous CD34+ stem cells (e.g.,mobilized in patients from the bone marrow into the peripheral blood viagranulocyte colony-stimulating factor (GCSF) administration). The CD34+cells can be harvested, purified, cultured, and the nucleases and/orIL2RG and/or RAG (RAG1 or RAG2) donor (e.g., an adenoviral vector donor)introduced into the cell by any suitable method.

In another aspect, the methods and compositions of the invention providefor the use of cells, cell lines and animals (e.g., transgenic animals)in the screening of drug libraries and/or other therapeutic compositions(i.e., antibodies, structural RNAs, etc.) for use in treatment of X-SCIDor Omenn Syndrome. Such screens can begin at the cellular level withmanipulated cell lines or primary cells, and can progress up to thelevel of treatment of a whole animal (e.g., human). Thus, in certainaspects, described herein is a method of treating and/or preventingX-SCID or Omenn Syndrome in a subject in need thereof, the methodcomprising administering one or more nucleases, polynucleotides and/orcells as described herein to the subject. In certain embodiments, a cellas described herein (e.g., a cell comprising an IL2RG, RAG1 or RAG2transgene) is administered to the subject. In any of the methodsdescribed herein, the cell may be a stem cell derived from the subject(patient-derived stem cell).

In any of the compositions and methods described herein, the nucleasesare introduced in mRNA form and/or using one or more non-viral or viralvector(s). In certain embodiments, the nuclease(s) are introduced inmRNA form. In other embodiments, the IL2RG and/or RAG (RAG1 or RAG2)transgene is introduced using a viral vector, for instance anadeno-associated vector (AAV) including AAV1, AAV3, AAV4, AAV5, AAV6,AAV8, AAV 8.2, AAV9, AAV rh10, AAV2/8, AAV2/5 and AAV2/6, or via alentiviral or integration-defective lentiviral vector, and thenuclease(s) is(are) introduced in mRNA form. In still furtherembodiments, the nuclease(s) and donors are both introduced using one ormore viral or non-viral vectors. The nuclease and donor may be carriedon the same vector, on different vectors of the same type or ondifferent vectors of different types. In certain embodiments, thenuclease(s) is(are) introduced in mRNA form (e.g., via electroporation)and the donor is introduced using an AAV (e.g., AAV2/6), lentivirus orintegration defective lentivirus. In certain embodiments the donor isintroduced as single-stranded DNA.

The nuclease(s) and donors may be introduced concurrently or in order.When introduced sequentially, any time period (e.g., seconds to hours)may elapse between administration of the nucleases and donors. Incertain embodiments, the donors are introduced and after 12-36 hours (orany time therebetween), the nuclease are introduced into the cell. Incertain embodiments, the modified cells are incubated for hours to days(or any time therebetween) and then are aliquoted and frozen.

The IL2RG and/or RAG (RAG1 or RAG2) donor may be delivered to any celland integrated at any suitable gene. In certain embodiments, theendogenous gene is an IL2RG and/or RAG (RAG1 or RAG2) gene. In otherembodiments, the nuclease targets a safe harbor gene such as HPRT, CCR5,AAVS1, Rosa26, ALB or the like. In certain embodiments, the IL2RG and/orRAG (RAG1 or RAG2) donor is integrated into an HPRT locus such thatendogenous HPRT expression is inactivated and IL2RG and/or RAG (RAG1 orRAG2) is expressed from the HPRT locus (e.g., the donor includes controland regulatory elements necessary for expression). The resultingknockout of HPRT would allow for 6-thioguanine (6-TG) negative selectionof cells not harboring the corrective IL2RG, RAG1 and/or RAG2 donor atthe HPRT locus, for example in cases where levels of engraftment ofCD34+ cells with the corrective IL2RG, RAG1 and/or RAG2 transgenecassette are low and/or if the initial level of modification of thesecells is not sufficient.

Any cell can be modified using the compositions and methods of theinvention, including but not limited to prokaryotic or eukaryotic cellssuch as bacterial, insect, yeast, fish, mammalian (including non-humanmammals), and plant cells. In certain embodiments, the cell is an immunecell, for example a T-cell (e.g., CD4+, CD3+, CD8+, etc.), a dendriticcell, a B cell or the like. In other embodiments, the cell is apluripotent, totipotent or multipotent stem cell, for example an inducedpluripotent stem cell (iPSC), hematopoietic stem cells (e.g., CD34+), anembryonic stem cell or the like. In any of the methods or compositionsdescribed herein, the cell containing the IL2RG-encoding transgene canbe a stem or progenitor cell. Specific stem cell types that may be usedwith the methods and compositions of the invention include embryonicstem cells (ESC), induced pluripotent stem cells (iPSC) andhematopoietic stem cells (e.g., CD34+ cells). The iPSCs can be derivedfrom patient samples and from normal controls wherein the patientderived iPSC can be mutated to the normal or wild type gene sequence atthe gene of interest, or normal cells can be altered to the knowndisease allele at the gene of interest. Similarly, the hematopoieticstem cells can be isolated from a patient (e.g., a SCID patient with amutant form of one or more SCID-related genes such as IL2RG and/or Rag)or from a donor. These cells are then engineered to express functionalSCID-related protein(s) such as IL2RG or Rag (e.g., Rag1 or Rag2),expanded and then reintroduced into the patient. In certain embodiments,the cell is a patient derived hematopoietic stem cell. In otherembodiments, the cell is a COS, CHO (e.g., CHO-S, CHO-K1, CHO-DG44,CHO-DUXB11, CHO-DUKX, CHOK1SV), VERO, MDCK, WI38, V79, B14AF28-G3, BHK,HaK, NS0, SP2/0-Ag14, HeLa, HEK293 (e.g., HEK293-F, HEK293-H, HEK293-T),and perC6 cells.

A kit, comprising the nucleic acids, proteins and/or cells of theinvention, is also provided. The kit may comprise nucleic acids encodingthe nucleases, (e.g. RNA molecules or ZFN, TALEN, TtAgo or CRISPR/Cassystem encoding genes contained in a suitable expression vector), oraliquots of the nuclease proteins, donor molecules, suitable stemnessmodifiers, cells, instructions for performing the methods of theinvention, and the like.

These and other aspects will be readily apparent to the skilled artisanin light of disclosure as a whole.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 (SEQ ID NO:101) is a schematic representation of theIL2RG-specific nuclease target sites in Exon 1 and Intron 1 of theendogenous IL2RG gene. Darker grey bars indicate Exons 1 and 2, whilethe shorter light grey bars indicate the target sites for the nucleases.

FIG. 2 shows the result of a Surveyor™ nuclease digestion of PCRamplicons of the IL2RG locus after treatment of K562 cells with theindicated ZFNs and TALENs. GFP1 and GFP2 are control lanes where thecells have been transfected with GFP encoding vectors.

FIGS. 3A and 3B shows the result of a Surveyor™ nuclease digestion ofPCR amplicons of the IL2RG locus after treatment of CD34+ HSPCs cellswith the indicated ZFNs and TALENs. FIG. 3A shows activity results ofexemplary ZFNs in gel format (percent indels indicated beneath eachlane) and FIG. 3B is a table showing activity (indels) of the indicatedpairs.

FIGS. 4A and 4B are graphs depicting results of methylcellulose assayson CD34+ cells nucleofected with the nucleases. FIG. 4A depicts resultswith indicated ZFNs and TALENs. FIG. 4B shows results using the ZFN pair44298/44271 (IL2RG specific ZFN, 4 μg). The left most bar of each groupin each Figure shows colony forming units (erythroid) (CFU-E); the barsecond from the left in each group shows burst forming erythroid units(BFU-E); the bar second from the right in each group shows colonyforming units (granulocyte, monocyte) (CFU-GM); and the right most barof each groups shows pluripotent colony forming units (granulocyte,erythrocyte, monocyte, megakaryocyte) (CFU-GEMM).

FIGS. 5A through 5D are schematics depicting the IL2RG gene with commonmutations found in X-SCID patients (FIG. 5A); an exemplary donor withhomology arms flanking the ZFN or TALEN cleavage site in intron 1, a 5′splice acceptor, and polyA tail to terminate transcription (FIG. 5B);and an exemplary intron 1 donor with a 2A-GFP construct to assaytargeted integration and expression at the endogenous IL2RG locus viaflow cytometry or other fluorescence detection assays (FIG. 5C). FIG. 5Dis an illustration depicting the expression of a wild-type IL2RG proteinfollowing integration of the IL2RG exon 2-8 transgene donor into theendogenous IL2RG intron 1.

FIGS. 6A and 6B are graphs depicting IL2RG mRNA levels in Jurkat cellstreated with the indicated nucleases and/or donors. FIG. 6A shows IL2RGmRNA expression in the indicated cells. FIG. 6B depicts results of Miseqhigh-throughput DNA sequencing analysis and shows the percentmodification in the indicated cells. “A” and “B” donors are identicalexcept B contains a 3′ Miseq primer binding sequence to assay TI by nextgeneration sequencing. “Z” refers to ZFNs, “T” refers to TALENs, and “N”refers to naïve cells.

FIGS. 7A and 7B depict detection of targeted integration of a 6 basepair RFLP sequence by restriction enzyme digestion of a PCR amplicon ofgenomic DNA from K562 cells treated with a 106 base pair single-strandedoligonucleotide donor and the indicated nucleases. “F” indicates use ofa forward-strand donor, “R” use of a reverse-strand donor. FIG. 7A showsresults from cells harvested 3 days post nucleofection; FIG. 7B showsresults from cells harvested 10 days post nucleofection.

FIGS. 8A and 8B depict detection of targeted integration of a 6 basepair RFLP sequence by restriction enzyme digestion of a PCR amplicon ofgenomic DNA from CD34+ HSPCs treated with a 106 base pairsingle-stranded oligonucleotide donor and the indicated nucleases. “F”indicates use of a forward-strand donor, “R” use of a reverse-stranddonor. FIG. 8A shows results from cells harvested 3 days postnucleofection; FIG. 8B shows results from cells harvested 10 days postnucleofection.

FIGS. 9A and 9B depict detection of targeted integration 3 dayspost-nucleofection of a 6 base pair RFLP sequence by restriction enzymedigestion of a PCR amplicon of genomic DNA from K562 and CD34+ HSPCstreated with a 106 base pair oligonucleotide donor and the indicatednucleases. FIG. 9A shows results from K562 cells; FIG. 9B shows resultsfrom CD34+ HSPCs.

FIGS. 10A and 10B depict detection of targeted integration 10 dayspost-nucleofection of a 6 base pair RFLP sequence by restriction enzymedigestion of a PCR amplicon of genomic DNA from K562 and CD34+ HSPCstreated with a 106 base pair oligonucleotide donor and with theindicated nucleases. FIG. 10A shows results from K562 cells; FIG. 9Bshows results from CD34+ HSPCs

FIGS. 11A and 11B depict targeted integration of an exemplary correctivepartial IL2RG cDNA donor in CD34+ cells using the ZFN pair 44271/44298delivered as mRNA. FIG. 11A is a gel showing PCR using primers targetingoutside the region of homology of the donor, thus generating bothwild-type and TI (larger) products. A donor-specific restriction enzymefragmented the larger molecular weight product (right part of the gel),indicating it was indeed the correct TI product. The percentage ofindels (“% indels) (insertions and/or deletions following nucleasecleavage) listed are from parallel high-throughput DNA sequencinganalysis. FIG. 11B shows PCR amplification of the same set of samplesusing either ethidium bromide (left, 30 cycles of PCR) or theincorporation of radioactive nucleotides (right, 23 cycles of PCR) todetect the DNA. Use of fewer PCR cycles prevents formation ofheteroduplex DNA between different alleles of IL2RG and gives a superiorsignal to noise ratio for detection of targeted integration. Levels ofTI (“% TI”) are shown below % indels.

FIG. 12 is a graph depicting targeted integration of corrective partialIL2RG cDNA donor in CD34+ cells analyzed by next generation sequencing.Miseq analysis of NHEJ and TI in CD34 cells yield >50% indels and ˜10%TI in cells treated with the ZFN pair 44271/44298 and AAV6 partial IL2RGcDNA donor (grey plus signs), which is stable 2 to 5 days posttransfection. Black plus signs indicate SA-2A-GFP donor.

FIGS. 13A and 13B are graphs depicting methylcellulose assay andhigh-throughput DNA sequencing analysis of individual CD34-derived cellclones. FIG. 13A shows number of colonies formed following treatmentwith the ZFN pair 44271/44298 delivered as mRNA, IL2RG partial cDNAdonor delivered with AAV6, or both. GFP mRNA was delivered as a control.The left most bar of each group shows colony forming units (erythroid)(CFU-E); the bar second from the left in each group shows burst formingerythroid units (BFU-E); the bar second from the right in each groupshows colony forming units (granulocyte, monocyte) (CFU-GM); and theright most bar of each groups shows pluripotent colony forming units(granulocyte, erythrocyte, monocyte, megakaryocyte) (CFU-GEMM). FIG. 13Bshows the percent of modified alleles (targeted integration shown inwhite portions of the bars, indels following NHEJ shown in shaded at thebottom of each bar) under the indicated conditions.

FIGS. 14A and 14B are graphs depicting targeted integration of anexemplary corrective partial IL2RG cDNA donor into CD34+ cells usingMaxcyte electroporation, including cryopreserved cells modified with theZFN pair 44271/44298 delivered as mRNA and a corrective partial IL2RGcDNA donor delivered with AAV6. FIG. 14A shows the percent of viablecells before and after cryopreservation under the indicated conditions.The left most bar in each group shows percent viability at day 0 beforethawing; the middle bar shows percent viability at day 0 post-thawing;and the right most bar in each group shows the percent viability at day3 post-thawing. FIG. 14B shows the percent of modified alleles (targetedintegration shown in white portions of the bars at the top of the bars,indels following NHEJ shown in shaded at the bottom of each bar) underthe indicated conditions. The percent of TI detected is indicated bywhite boxes. In some samples, (ZFNs, Day 0 Prethaw; GFP—Day 3 Post Thaw;and ZFNs—Day 3 Post Thaw), the signal represented by white boxes is verylow such that the boxes are compressed to a black line.

FIGS. 15A and 15B are schematics depicting the RAG genes. FIG. 15Adepicts the RAG1 gene were the gene comprises three exons and twointrons, where variable splicing results in two isoforms, either exon 1linked to exon 3 (isoform 1) or exon 2 linked to exon 3 (isoform 2). Thesequences encoding the Rag1 polypeptide are found in exon 3. FIG. 15Bdepicts the RAG2 gene which also comprises three exons and two introns.Variable splicing also results in two isoforms, either exon 1 linked toexon 3 (isoform 1) or exon 1 linked to exon 2 and exon 3 (isoform 3).

FIGS. 16A and 16B are schematics depicting the method used to correctRAG1 gene mutations. FIG. 16A shows an exemplary donor with homologyarms flanking the ZFN cleavage site in intron 2, a 5′ splice acceptor,and polyA tail to terminate transcription. Also shown are the locationsof the two ZFN target sites in intron 2. FIG. 16B is an illustrationdepicting the splicing of a wild-type RAG1 transcript for the two RAG1isoforms following integration of the RAG1 cDNA transgene donor into theendogenous RAG1 intron 2.

FIG. 17A through 17C are graphs related to assaying functionalcorrection of mature spliced RAG1 transcripts in K562 cells. FIG. 17Adepicts the qPCR scheme of discriminating between the wild-type and thecodon-optimized corrective cDNA transgene for RAG1 isoform 1. FIG. 17Bshows the percentage of exogenous codon-optimized RAG1 transcriptsrelative to wild-type RAG1 transcripts. FIG. 17C shows Miseq analysis ofthese same samples and indicates ˜5% targeted integration of thecorrective RAG1 transgene yields ˜6% total levels of correct, fullymaturely spliced RAG1 transcripts. The ZFN pair used in theseexperiments was the Site 4 specific ZFN pair 50773/49812.

FIGS. 18A and 18B depict targeted integration of an exemplary correctiveRAG1 cDNA donor in CD34+ cells using BTX electroporation. FIG. 18A showsresults with cryopreserved cells modified with either the “Site 1” ZFNpair (50698/50718). FIG. 18B shows results using the “Site 4” ZFN pair(50773/49812) delivered as mRNA and a corrective RAG1 cDNA donordelivered with AAV6. Data shown is from 1 day post transfection(“1DPT”).

FIGS. 19A and 19B are graphs depicting targeted integration of anexemplary corrective RAG1 cDNA donor into CD34+ cells using Maxcyteelectroporation, including cells modified with either the “Site 1” ZFNpair (50698/50718) or the “Site 4” ZFN pair (50773/49812) delivered asmRNA where the corrective RAG1 cDNA donor was delivered with AAV6. FIG.19A shows the percent of viable cells before cryopreservation under theindicated conditions. FIG. 19B shows the percent of modified allelesunder the indicated conditions. The percent of TI detected is indicatedby grey boxes.

DETAILED DESCRIPTION

Disclosed herein are compositions and methods for targeted integrationof a corrective SCID-related protein (e.g., IL2RG, RAG1 or RAG2)transgene into a cell (e.g., lymphocyte precursors such as CD34+hematopoietic stem cells). The cells are suitable for infusion intosevere combined immunodeficiency (X-SCID or SCID) patients such thatsubsequent in vivo differentiation of these precursors into cellsexpressing the functional proteins lacking or deficient in the subjectwith a SCID disorder is provided by the cell, which cells can treatand/or prevent disease in the recipient SCID patient. Cells comprisingan IL2RG transgene are suitable for infusion into X-SCID patients suchthat subsequent in vivo differentiation of these stem cells into cellsthat express the functional IL2RG protein treat and/or prevent X-SCIDdisease in the patient. Similarly, stem cells comprising the RAG1 orRAG2 transgenes are suitable for infusion into Omenn Syndrome patientssuch that subsequent in vivo differentiation of these precursors intocells expression the functional Rag1 and/or Rag2 proteins treats and/orprevents disease in an Omenn Syndrome patient.

Targeted integration of IL2RG, RAG1 or RAG2 (e.g., into intronic regionsof IL2RG, RAG1 and/or RAG2 and/or a safe harbor gene) avoids the issuesassociated with gene therapy methods that involve random integration ofIL2RG, RAG1 or RAG2 into the genome as well as methods that involveintegration into exons of IL2RG, RAG1 or RAG2. In particular, randomintegration often results in adverse events due to the partiallytranscribed upstream region of the locus and, in addition, intronicinsertion at the IL2RG, RAG1 or RAG2 locus utilizes the endogenoustranscriptional regulatory elements such as native RNA splicing,promoters, and enhancers which least invasively replaces the defectivelocus with a correct form.

The invention contemplates the integration of a donor comprising anyfunctional IL2RG or Rag protein, including a functional fragment ofthese proteins such as a partial cDNA comprising exons 2-8 of the IL2RGgene, a splice acceptor sequence and a polyadenylation sequence. Alsocontemplated is the integration of a donor comprising a full cDNAcomprising exon 3 of RAG1 or RAG2, a splice acceptor sequence and apolyadenylation sequence. Targeted integration of the IL2RG donor intointron 1 of the endogenous IL2RG will result in the expression of awild-type IL2RG or common gamma protein, thus treating or preventingX-SCID. Targeted integration of the RAG1 or RAG2 donor into intron 2 ofthe endogenous RAG1 or RAG 2 gene, respectively, will result in theexpression of wild type Rag1 or Rag2, thus treating or preventing OmennSyndrome.

General

Practice of the methods, as well as preparation and use of thecompositions disclosed herein employ, unless otherwise indicated,conventional techniques in molecular biology, biochemistry, chromatinstructure and analysis, computational chemistry, cell culture,recombinant DNA and related fields as are within the skill of the art.These techniques are fully explained in the literature. See, forexample, Sambrook et al. MOLECULAR CLONING: A LABORATORY MANUAL, Secondedition, Cold Spring Harbor Laboratory Press, 1989 and Third edition,2001; Ausubel et al., CURRENT PROTOCOLS IN MOLECULAR BIOLOGY, John Wiley& Sons, New York, 1987 and periodic updates; the series METHODS INENZYMOLOGY, Academic Press, San Diego; Wolffe, CHROMATIN STRUCTURE ANDFUNCTION, Third edition, Academic Press, San Diego, 1998; METHODS INENZYMOLOGY, Vol. 304, “Chromatin” (P. M. Wassarman and A. P. Wolffe,eds.), Academic Press, San Diego, 1999; and METHODS IN MOLECULARBIOLOGY, Vol. 119, “Chromatin Protocols” (P. B. Becker, ed.) HumanaPress, Totowa, 1999.

Definitions

The terms “nucleic acid,” “polynucleotide,” and “oligonucleotide” areused interchangeably and refer to a deoxyribonucleotide orribonucleotide polymer, in linear or circular conformation, and ineither single- or double-stranded form. For the purposes of the presentdisclosure, these terms are not to be construed as limiting with respectto the length of a polymer. The terms can encompass known analogues ofnatural nucleotides, as well as nucleotides that are modified in thebase, sugar and/or phosphate moieties (e.g., phosphorothioatebackbones). In general, an analogue of a particular nucleotide has thesame base-pairing specificity; i.e., an analogue of A will base-pairwith T.

The terms “polypeptide,” “peptide” and “protein” are usedinterchangeably to refer to a polymer of amino acid residues. The termalso applies to amino acid polymers in which one or more amino acids arechemical analogues or modified derivatives of a correspondingnaturally-occurring amino acids.

“Binding” refers to a sequence-specific, non-covalent interactionbetween macromolecules (e.g., between a protein and a nucleic acid). Notall components of a binding interaction need be sequence-specific (e.g.,contacts with phosphate residues in a DNA backbone), as long as theinteraction as a whole is sequence-specific. Such interactions aregenerally characterized by a dissociation constant (K_(d)) of 10⁻⁶ M⁻¹or lower. “Affinity” refers to the strength of binding: increasedbinding affinity being correlated with a lower K_(d).

A “binding protein” is a protein that is able to bind to anothermolecule. A binding protein can bind to, for example, a DNA molecule (aDNA-binding protein), an RNA molecule (an RNA-binding protein) and/or aprotein molecule (a protein-binding protein). In the case of aprotein-binding protein, it can bind to itself (to form homodimers,homotrimers, etc.) and/or it can bind to one or more molecules of adifferent protein or proteins. A binding protein can have more than onetype of binding activity. For example, zinc finger proteins haveDNA-binding, RNA-binding and protein-binding activity.

A “zinc finger DNA binding protein” (or binding domain) is a protein, ora domain within a larger protein, that binds DNA in a sequence-specificmanner through one or more zinc fingers, which are regions of amino acidsequence within the binding domain whose structure is stabilized throughcoordination of a zinc ion. The term zinc finger DNA binding protein isoften abbreviated as zinc finger protein or ZFP.

A “TALE DNA binding domain” or “TALE” is a polypeptide comprising one ormore TALE repeat domains/units. The repeat domains are involved inbinding of the TALE to its cognate target DNA sequence. A single “repeatunit” (also referred to as a “repeat”) is typically 33-35 amino acids inlength and exhibits at least some sequence homology with other TALErepeat sequences within a naturally occurring TALE protein.

Zinc finger and TALE binding domains can be “engineered” to bind to apredetermined nucleotide sequence, for example via engineering (alteringone or more amino acids) of the recognition helix region of a naturallyoccurring zinc finger or TALE protein. Therefore, engineered DNA bindingproteins (zinc fingers or TALEs) are proteins that are non-naturallyoccurring. Non-limiting examples of methods for engineering DNA-bindingproteins are design and selection. A designed DNA binding protein is aprotein not occurring in nature whose design/composition resultsprincipally from rational criteria. Rational criteria for design includeapplication of substitution rules and computerized algorithms forprocessing information in a database storing information of existing ZFPand/or TALE designs and binding data. See, for example, U.S. Pat. Nos.6,140,081; 6,453,242; 6,534,261 and 8,586,526: sec also WO 98/53058; WO98/53059: WO 98/53060; WO 02/016536 and WO 03/016496.

A “selected” zinc finger protein or TALE is a protein not found innature whose production results primarily from an empirical process suchas phage display, interaction trap or hybrid selection. See e.g., U.S.Pat. Nos. 5,789,538; 5,925,523; 6,007,988; 6,013,453; 6,200,759;8,586,526; WO 95/19431; WO 96/06166; WO 98/53057; WO 98/54311; WO00/27878; WO 01/60970 WO 01/88197, WO 02/099084.

“TtAgo” is a prokaryotic Argonaute protein thought to be involved ingene silencing. TtAgo is derived from the bacteria Thermus thermophilus.See, e.g., Swarts et al, ibid, G. Sheng et al., (2013) Proc. Natl. Acad.Sci. U.S.A. 111, 652). A “TtAgo system” is all the components requiredincluding, for example, guide DNAs for cleavage by a TtAgo enzyme.

“Recombination” refers to a process of exchange of genetic informationbetween two polynucleotides, including but not limited to, donor captureby non-homologous end joining (NHEJ) and homologous recombination. Forthe purposes of this disclosure, “homologous recombination (HR)” refersto the specialized form of such exchange that takes place, for example,during repair of double-strand breaks in cells via homology-directedrepair mechanisms. This process requires nucleotide sequence homology,uses a “donor” molecule to template repair of a “target” molecule (i.e.,the one that experienced the double-strand break), and is variouslyknown as “non-crossover gene conversion” or “short tract geneconversion,” because it leads to the transfer of genetic informationfrom the donor to the target. Without wishing to be bound by anyparticular theory, such transfer can involve mismatch correction ofheteroduplex DNA that forms between the broken target and the donor,and/or “synthesis-dependent strand annealing,” in which the donor isused to resynthesize genetic information that will become part of thetarget, and/or related processes. Such specialized HR often results inan alteration of the sequence of the target molecule such that part orall of the sequence of the donor polynucleotide is incorporated into thetarget polynucleotide.

In the methods of the disclosure, one or more targeted nucleases asdescribed herein create a double-stranded break (DSB) in the targetsequence (e.g., cellular chromatin) at a predetermined site. The DSB mayresult in deletions and/or insertions by homology-directed repair or bynon-homology-directed repair mechanisms. Deletions may include anynumber of base pairs. Similarly, insertions may include any number ofbase pairs including, for example, integration of a “donor”polynucleotide, optionally having homology to the nucleotide sequence inthe region of the break. The donor sequence may be physically integratedor, alternatively, the donor polynucleotide is used as a template forrepair of the break via homologous recombination, resulting in theintroduction of all or part of the nucleotide sequence as in the donorinto the cellular chromatin. Thus, a first sequence in cellularchromatin can be altered and, in certain embodiments, can be convertedinto a sequence present in a donor polynucleotide. Thus, the use of theterms “replace” or “replacement” can be understood to representreplacement of one nucleotide sequence by another, (i.e., replacement ofa sequence in the informational sense), and does not necessarily requirephysical or chemical replacement of one polynucleotide by another.

In any of the methods described herein, additional pairs of zinc-fingerproteins, TALENs, TtAgo or CRISPR/Cas systems can be used for additionaldouble-stranded cleavage of additional target sites within the cell.

Any of the methods described herein can be used for insertion of a donorof any size and/or partial or complete inactivation of one or moretarget sequences in a cell by targeted integration of donor sequencethat disrupts expression of the gene(s) of interest. Cell lines withpartially or completely inactivated genes are also provided.

In any of the methods described herein, the exogenous nucleotidesequence (the “donor sequence” or “transgene”) can contain sequencesthat are homologous, but not identical, to genomic sequences in theregion of interest, thereby stimulating homologous recombination toinsert a non-identical sequence in the region of interest. Thus, incertain embodiments, portions of the donor sequence that are homologousto sequences in the region of interest exhibit between about 80 to 99%(or any integer therebetween) sequence identity to the genomic sequencethat is replaced. In other embodiments, the homology between the donorand genomic sequence is higher than 99%, for example if only 1nucleotide differs as between donor and genomic sequences of over 100contiguous base pairs. In certain cases, a non-homologous portion of thedonor sequence can contain sequences not present in the region ofinterest, such that new sequences are introduced into the region ofinterest. In these instances, the non-homologous sequence is generallyflanked by sequences of 50-1,000 base pairs (or any integral valuetherebetween) or any number of base pairs greater than 1,000, that arehomologous or identical to sequences in the region of interest. In otherembodiments, the donor sequence is non-homologous to the first sequence,and is inserted into the genome by non-homologous recombinationmechanisms.

“Cleavage” refers to the breakage of the covalent backbone of a DNAmolecule. Cleavage can be initiated by a variety of methods including,but not limited to, enzymatic or chemical hydrolysis of a phosphodiesterbond. Both single-stranded cleavage and double-stranded cleavage arepossible, and double-stranded cleavage can occur as a result of twodistinct single-stranded cleavage events. DNA cleavage can result in theproduction of either blunt ends or staggered ends. In certainembodiments, fusion polypeptides are used for targeted double-strandedDNA cleavage.

A “cleavage half-domain” is a polypeptide sequence which, in conjunctionwith a second polypeptide (either identical or different) forms acomplex having cleavage activity (preferably double-strand cleavageactivity). The terms “first and second cleavage half-domains;” “+ and −cleavage half-domains” and “right and left cleavage half-domains” areused interchangeably to refer to pairs of cleavage half-domains thatdimerize.

An “engineered cleavage half-domain” is a cleavage half-domain that hasbeen modified so as to form obligate heterodimers with another cleavagehalf-domain (e.g., another engineered cleavage half-domain). See, also,U.S. Pat. Nos. 8,623,618; 7,888,121; 7,914,796; and 8,034,598 and U.S.Publication No. 20110201055, incorporated herein by reference in theirentireties.

The term “sequence” refers to a nucleotide sequence of any length, whichcan be DNA or RNA; can be linear, circular or branched and can be eithersingle-stranded or double stranded. The term “donor sequence” refers toa nucleotide sequence that is inserted into a genome. A donor sequencecan be of any length, for example between 2 and 100,000,000 nucleotidesin length (or any integer value therebetween or thereabove), preferablybetween about 100 and 100,000 nucleotides in length (or any integertherebetween), more preferably between about 2000 and 20,000 nucleotidesin length (or any value therebetween) and even more preferable, betweenabout 5 and 15 kb (or any value therebetween).

“Chromatin” is the nucleoprotein structure comprising the cellulargenome. Cellular chromatin comprises nucleic acid, primarily DNA, andprotein, including histones and non-histone chromosomal proteins. Themajority of eukaryotic cellular chromatin exists in the form ofnucleosomes, wherein a nucleosome core comprises approximately 150 basepairs of DNA associated with an octamer comprising two each of histonesH2A, H2B, H3 and H4; and linker DNA (of variable length depending on theorganism) extends between nucleosome cores. A molecule of histone H1 isgenerally associated with the linker DNA. For the purposes of thepresent disclosure, the term “chromatin” is meant to encompass all typesof cellular nucleoprotein, both prokaryotic and eukaryotic. Cellularchromatin includes both chromosomal and episomal chromatin.

A “chromosome,” is a chromatin complex comprising all or a portion ofthe genome of a cell. The genome of a cell is often characterized by itskaryotype, which is the collection of all the chromosomes that comprisethe genome of the cell. The genome of a cell can comprise one or morechromosomes.

An “episome” is a replicating nucleic acid, nucleoprotein complex orother structure comprising a nucleic acid that is not part of thechromosomal karyotype of a cell. Examples of episomes include plasmidsand certain viral genomes.

An “accessible region” is a site in cellular chromatin in which a targetsite present in the nucleic acid can be bound by an exogenous moleculewhich recognizes the target site. Without wishing to be bound by anyparticular theory, it is believed that an accessible region is one thatis not packaged into a nucleosomal structure. The distinct structure ofan accessible region can often be detected by its sensitivity tochemical and enzymatic probes, for example, nucleases.

A “target site” or “target sequence” is a nucleic acid sequence thatdefines a portion of a nucleic acid to which a binding molecule willbind, provided sufficient conditions for binding exist.

An “exogenous” molecule is a molecule that is not normally present in acell, but can be introduced into a cell by one or more genetic,biochemical or other methods. “Normal presence in the cell” isdetermined with respect to the particular developmental stage andenvironmental conditions of the cell. Thus, for example, a molecule thatis present only during embryonic development of muscle is an exogenousmolecule with respect to an adult muscle cell. Similarly, a moleculeinduced by heat shock is an exogenous molecule with respect to anon-heat-shocked cell. An exogenous molecule can comprise, for example,a functioning version of a malfunctioning endogenous molecule or amalfunctioning version of a normally-functioning endogenous molecule.

An exogenous molecule can be, among other things, a small molecule, suchas is generated by a combinatorial chemistry process, or a macromoleculesuch as a protein, nucleic acid, carbohydrate, lipid, glycoprotein,lipoprotein, polysaccharide, any modified derivative of the abovemolecules, or any complex comprising one or more of the above molecules.Nucleic acids include DNA and RNA, can be single- or double-stranded;can be linear, branched or circular; and can be of any length. Nucleicacids include those capable of forming duplexes, as well astriplex-forming nucleic acids. See, for example, U.S. Pat. Nos.5,176,996 and 5,422,251. Proteins include, but are not limited to,DNA-binding proteins, transcription factors, chromatin remodelingfactors, methylated DNA binding proteins, polymerases, methylases,demethylases, acetylases, deacetylases, kinases, phosphatases,integrases, recombinases, ligases, topoisomerases, gyrases andhelicases.

An exogenous molecule can be the same type of molecule as an endogenousmolecule, e.g., an exogenous protein or nucleic acid. For example, anexogenous nucleic acid can comprise an infecting viral genome, a plasmidor episome introduced into a cell, or a chromosome that is not normallypresent in the cell. Methods for the introduction of exogenous moleculesinto cells are known to those of skill in the art and include, but arenot limited to, lipid-mediated transfer (i.e., liposomes, includingneutral and cationic lipids), electroporation, direct injection, cellfusion, particle bombardment, calcium phosphate co-precipitation,DEAE-dextran-mediated transfer and viral vector-mediated transfer. Anexogenous molecule can also be the same type of molecule as anendogenous molecule but derived from a different species than the cellis derived from. For example, a human nucleic acid sequence may beintroduced into a cell line originally derived from a mouse or hamster.Methods for the introduction of exogenous molecules into plant cells areknown to those of skill in the art and include, but are not limited to,protoplast transformation, silicon carbide (e.g., WHISKERS™),Agrobacterium-mediated transformation, lipid-mediated transfer (i.e.,liposomes, including neutral and cationic lipids), electroporation,direct injection, cell fusion, particle bombardment (e.g., using a “genegun”), calcium phosphate co-precipitation, DEAE-dextran-mediatedtransfer and viral vector-mediated transfer.

By contrast, an “endogenous” molecule is one that is normally present ina particular cell at a particular developmental stage under particularenvironmental conditions. For example, an endogenous nucleic acid cancomprise a chromosome, the genome of a mitochondrion, chloroplast orother organelle, or a naturally-occurring episomal nucleic acid.Additional endogenous molecules can include proteins, for example,transcription factors and enzymes.

As used herein, the term “product of an exogenous nucleic acid” includesboth polynucleotide and polypeptide products, for example, transcriptionproducts (polynucleotides such as RNA) and translation products(polypeptides).

A “fusion” molecule is a molecule in which two or more subunit moleculesare linked, preferably covalently. The subunit molecules can be the samechemical type of molecule, or can be different chemical types ofmolecules. Examples of the first type of fusion molecule include, butare not limited to, fusion proteins (for example, a fusion between a ZFPor TALE DNA-binding domain and one or more activation domains) andfusion nucleic acids (for example, a nucleic acid encoding the fusionprotein described supra). Examples of the second type of fusion moleculeinclude, but are not limited to, a fusion between a triplex-formingnucleic acid and a polypeptide, and a fusion between a minor groovebinder and a nucleic acid.

Expression of a fusion protein in a cell can result from delivery of thefusion protein to the cell or by delivery of a polynucleotide encodingthe fusion protein to a cell, wherein the polynucleotide is transcribed,and the transcript is translated, to generate the fusion protein.Trans-splicing, polypeptide cleavage and polypeptide ligation can alsobe involved in expression of a protein in a cell. Methods forpolynucleotide and polypeptide delivery to cells are presented elsewherein this disclosure.

A “gene,” for the purposes of the present disclosure, includes a DNAregion encoding a gene product (see infra), as well as all DNA regionswhich regulate the production of the gene product, whether or not suchregulatory sequences are adjacent to coding and/or transcribedsequences. Accordingly, a gene includes, but is not necessarily limitedto, promoter sequences, terminators, translational regulatory sequencessuch as ribosome binding sites and internal ribosome entry sites,enhancers, silencers, insulators, boundary elements, replicationorigins, matrix attachment sites and locus control regions.

“Gene expression” refers to the conversion of the information, containedin a gene, into a gene product. A gene product can be the directtranscriptional product of a gene (e.g., mRNA, tRNA, rRNA, antisenseRNA, ribozyme, structural RNA or any other type of RNA) or a proteinproduced by translation of an mRNA. Gene products also include RNAswhich are modified, by processes such as capping, polyadenylation,methylation, and editing, and proteins modified by, for example,methylation, acetylation, phosphorylation, ubiquitination,ADP-ribosylation, myristilation, and glycosylation.

“Modulation” of gene expression refers to a change in the activity of agene. Modulation of expression can include, but is not limited to, geneactivation and gene repression. Genome editing (e.g., cleavage,alteration, inactivation, random mutation) can be used to modulateexpression. Gene inactivation refers to any reduction in gene expressionas compared to a cell that does not include a ZFP, TALE, TtAgo orCRISPR/Cas system as described herein. Thus, gene inactivation may bepartial or complete.

A “region of interest” is any region of cellular chromatin, such as, forexample, a gene or a non-coding sequence within or adjacent to a gene,in which it is desirable to bind an exogenous molecule. Binding can befor the purposes of targeted DNA cleavage and/or targeted recombination.A region of interest can be present in a chromosome, an episome, anorganellar genome (e.g., mitochondrial, chloroplast), or an infectingviral genome, for example. A region of interest can be within the codingregion of a gene, within transcribed non-coding regions such as, forexample, leader sequences, trailer sequences or introns, or withinnon-transcribed regions, either upstream or downstream of the codingregion. A region of interest can be as small as a single nucleotide pairor up to 2,000 nucleotide pairs in length, or any integral value ofnucleotide pairs.

“Eukaryotic” cells include, but are not limited to, fungal cells (suchas yeast), plant cells, animal cells, mammalian cells and human cells(e.g., T-cells), including stem cells (pluripotent and multipotent).

The terms “operative linkage” and “operatively linked” (or “operablylinked”) are used interchangeably with reference to a juxtaposition oftwo or more components (such as sequence elements), in which thecomponents are arranged such that both components function normally andallow the possibility that at least one of the components can mediate afunction that is exerted upon at least one of the other components. Byway of illustration, a transcriptional regulatory sequence, such as apromoter, is operatively linked to a coding sequence if thetranscriptional regulatory sequence controls the level of transcriptionof the coding sequence in response to the presence or absence of one ormore transcriptional regulatory factors. A transcriptional regulatorysequence is generally operatively linked in cis with a coding sequence,but need not be directly adjacent to it. For example, an enhancer is atranscriptional regulatory sequence that is operatively linked to acoding sequence, even though they are not contiguous.

With respect to fusion polypeptides, the term “operatively linked” canrefer to the fact that each of the components performs the same functionin linkage to the other component as it would if it were not so linked.For example, with respect to a fusion polypeptide in which a ZFP, TALE,TtAgo or Cas DNA-binding domain is fused to an activation domain, theZFP, TALE, TtAgo or Cas DNA-binding domain and the activation domain arein operative linkage if, in the fusion polypeptide, the ZFP, TALE, TtAgoor Cas DNA-binding domain portion is able to bind its target site and/orits binding site, while the activation domain is able to upregulate geneexpression. When a fusion polypeptide in which a ZFP, TALE, TtAgo or CasDNA-binding domain is fused to a cleavage domain, the ZFP, TALE, TtAgoor Cas DNA-binding domain and the cleavage domain are in operativelinkage if, in the fusion polypeptide, the ZFP, TALE, TtAgo or CasDNA-binding domain portion is able to bind its target site and/or itsbinding site, while the cleavage domain is able to cleave DNA in thevicinity of the target site.

A “functional fragment” of a protein, polypeptide or nucleic acid is aprotein, polypeptide or nucleic acid whose sequence is not identical tothe full-length protein, polypeptide or nucleic acid, yet retains thesame function as the full-length protein, polypeptide or nucleic acid. Afunctional fragment can possess more, fewer, or the same number ofresidues as the corresponding native molecule, and/or can contain one ormore amino acid or nucleotide substitutions. Methods for determining thefunction of a nucleic acid (e.g., coding function, ability to hybridizeto another nucleic acid) are well-known in the art. Similarly, methodsfor determining protein function are well-known. For example, theDNA-binding function of a polypeptide can be determined, for example, byfilter-binding, electrophoretic mobility-shift, or immunoprecipitationassays. DNA cleavage can be assayed by gel electrophoresis. See Ausubelet al., supra. The ability of a protein to interact with another proteincan be determined, for example, by co-immunoprecipitation, two-hybridassays or complementation, both genetic and biochemical. See, forexample, Fields et al. (1989) Nature 340:245-246; U.S. Pat. No.5,585,245 and PCT WO 98/44350.

A “vector” is capable of transferring gene sequences to target cells.Typically, “vector construct,” “expression vector,” and “gene transfervector,” mean any nucleic acid construct capable of directing theexpression of a gene of interest and which can transfer gene sequencesto target cells. Thus, the term includes cloning, and expressionvehicles, as well as integrating vectors.

The terms “subject” and “patient” are used interchangeably and refer tomammals such as human patients and non-human primates, as well asexperimental animals such as rabbits, dogs, cats, rats, mice, and otheranimals. Accordingly, the term “subject” or “patient” as used hereinmeans any mammalian patient or subject to which the nucleases, donorsand/or genetically modified cells of the invention can be administered.Subjects of the present invention include those with a disorder.

“Stemness” refers to the relative ability of any cell to act in a stemcell-like manner, i.e., the degree of toti-, pluri-, or oligopotentcyand expanded or indefinite self-renewal that any particular stem cellmay have.

Fusion Molecules

Described herein are compositions, for example nucleases, that areuseful for cleavage of a selected target gene (e.g., IL2RG) in a cell.In certain embodiments, one or more components of the fusion molecules(e.g., nucleases) are naturally occurring. In other embodiments, one ormore of the components of the fusion molecules (e.g., nucleases) arenon-naturally occurring, i.e., engineered in the DNA-binding moleculesand/or cleavage domain(s). For example, the DNA-binding portion of anaturally-occurring nuclease may be altered to bind to a selected targetsite (e.g., a single guide RNA of a CRISPR/Cas system or a meganucleasethat has been engineered to bind to site different than the cognatebinding site). In other embodiments, the nuclease comprises heterologousDNA-binding and cleavage domains (e.g., zinc finger nucleases;TAL-effector domain DNA binding proteins; meganuclease DNA-bindingdomains with heterologous cleavage domains).

A. DNA-Binding Molecules

The fusion molecules described herein can include any DNA-bindingmolecule (also referred to as DNA-binding domain), including proteindomains and/or polynucleotide DNA-binding domains.

In certain embodiments, the composition and methods described hereinemploy a meganuclease (homing endonuclease) DNA-binding domain forbinding to the donor molecule and/or binding to the region of interestin the genome of the cell. Naturally-occurring meganucleases recognize15-40 base-pair cleavage sites and are commonly grouped into fourfamilies: the LAGLIDADG family (“LAGLIDADG” disclosed as SEQ ID NO: 96),the GIY-YIG family, the His-Cyst box family and the HNH family.Exemplary homing endonucleases include I-SceI, I-CeuI, PI-PspI, PI-Sce,I-SceIV, I-CsmI, I-PanI, I-SceII, I-PpoI, I-SceIII, I-CreI, I-TevI,I-TevII and I-TevIII. Their recognition sequences are known. See alsoU.S. Pat. No. 5,420,032; U.S. Pat. No. 6,833,252; Belfort et al. (1997)Nucleic Acids Res. 25:3379-3388; Dujon et al. (1989) Gene 82:115-118;Perler et al. (1994) Nucleic Acids Res. 22, 1125-1127; Jasin (1996)Trends Genet. 12:224-228; Gimble et al. (1996) J. Mol. Biol.263:163-180; Argast et al. (1998) J. Mol. Biol. 280:345-353 and the NewEngland Biolabs catalogue. In addition, the DNA-binding specificity ofhoming endonucleases and meganucleases can be engineered to bindnon-natural target sites. See, for example, Chevalier et al. (2002)Molec. Cell 10:895-905; Epinat et al. (2003) Nucleic Acids Res.31:2952-2962; Ashworth et al. (2006) Nature 441:656-659; Paques et al.(2007) Current Gene Therapy 7:49-66; U.S. Patent Publication No.20070117128. The DNA-binding domains of the homing endonucleases andmeganucleases may be altered in the context of the nuclease as a whole(i.e., such that the nuclease includes the cognate cleavage domain) ormay be fused to a heterologous cleavage domain.

In other embodiments, the DNA-binding domain of one or more of thenucleases used in the methods and compositions described hereincomprises a naturally occurring or engineered (non-naturally occurring)TAL effector DNA binding domain. See, e.g., U.S. Pat. No. 8,586,526,incorporated by reference in its entirety herein. The plant pathogenicbacteria of the genus Xanthomonas are known to cause many diseases inimportant crop plants. Pathogenicity of Xanthomonas depends on aconserved type III secretion (T3S) system which injects more than 25different effector proteins into the plant cell. Among these injectedproteins are transcription activator-like (TAL) effectors which mimicplant transcriptional activators and manipulate the plant transcriptome(see Kay et at (2007) Science 318:648-651). These proteins contain a DNAbinding domain and a transcriptional activation domain. One of the mostwell characterized TAL-effectors is AvrBs3 from Xanthomonas campestgrispv. Vesicatoria (see Bonas et at (1989) Mol Gen Genet 218: 127-136 andWO2010079430). TAL-effectors contain a centralized domain of tandemrepeats, each repeat containing approximately 34 amino acids, which arekey to the DNA binding specificity of these proteins. In addition, theycontain a nuclear localization sequence and an acidic transcriptionalactivation domain (for a review see Schornack S, et at (2006) J PlantPhysiol 163(3): 256-272). In addition, in the phytopathogenic bacteriaRalstonia solanacearum two genes, designated brg11 and hpx17 have beenfound that are homologous to the AvrBs3 family of Xanthomonas in the R.solanacearum biovar 1 strain GMI1000 and in the biovar 4 strain RS1000(See Heuer et at (2007) Appl and Envir Micro 73(13): 4379-4384). Thesegenes are 98.9% identical in nucleotide sequence to each other butdiffer by a deletion of 1,575 bp in the repeat domain of hpx17. However,both gene products have less than 40% sequence identity with AvrBs3family proteins of Xanthomonas. See, e.g., U.S. Pat. No. 8,586,526,incorporated by reference in its entirety herein.

Specificity of these TAL effectors depends on the sequences found in thetandem repeats. The repeated sequence comprises approximately 102 bp andthe repeats are typically 91-100% homologous with each other (Bonas etal, ibid). Polymorphism of the repeats is usually located at positions12 and 13 and there appears to be a one-to-one correspondence betweenthe identity of the hypervariable diresidues (RVD) at positions 12 and13 with the identity of the contiguous nucleotides in the TAL-effector'starget sequence (see Moscou and Bogdanove, (2009) Science 326:1501 andBoch et at (2009) Science 326:1509-1512). Experimentally, the naturalcode for DNA recognition of these TAL-effectors has been determined suchthat an HD sequence at positions 12 and 13 leads to a binding tocytosine (C), NG binds to T, NI to A, C, G or T, NN binds to A or G, andING binds to T. These DNA binding repeats have been assembled intoproteins with new combinations and numbers of repeats, to makeartificial transcription factors that are able to interact with newsequences and activate the expression of a non-endogenous reporter genein plant cells (Boch et al, ibid). Engineered TAL proteins have beenlinked to a FokI cleavage half domain to yield a TAL effector domainnuclease fusion (TALEN). See, e.g., U.S. Pat. No. 8,586,526; Christianet at ((2010)<Genetics epub 10.1534/genetics.110.120717). In certainembodiments, TALE domain comprises an N-cap and/or C-cap as described inU.S. Pat. No. 8,586,526.

In certain embodiments, the DNA binding domain of one or more of thenucleases used for in vivo cleavage and/or targeted cleavage of thegenome of a cell comprises a zinc finger protein. Preferably, the zincfinger protein is non-naturally occurring in that it is engineered tobind to a target site of choice. See, for example, See, for example,Beerli et al. (2002) Nature Biotechnol. 20:135-141; Pabo et al. (2001)Ann. Rev. Biochem. 70:313-340; Isalan et al. (2001) Nature Biotechnol.19:656-660; Segal et al. (2001) Curr. Opin. Biotechnol. 12:632-637; Chooet al. (2000) Curr. Opin. Struct. Biol. 10:411-416; U.S. Pat. Nos.6,453,242; 6,534,261; 6,599,692; 6,503,717; 6,689,558; 7,030,215;6,794,136; 7,067,317; 7,262,054; 7,070,934; 7,361,635; 7,253,273; andU.S. Patent Publication Nos. 2005/0064474; 2007/0218528; 2005/0267061,all incorporated herein by reference in their entireties.

An engineered zinc finger binding domain can have a novel bindingspecificity, compared to a naturally-occurring zinc finger protein.Engineering methods include, but are not limited to, rational design andvarious types of selection. Rational design includes, for example, usingdatabases comprising triplet (or quadruplet) nucleotide sequences andindividual zinc finger amino acid sequences, in which each triplet orquadruplet nucleotide sequence is associated with one or more amino acidsequences of zinc fingers which bind the particular triplet orquadruplet sequence. See, for example, co-owned U.S. Pat. Nos. 6,453,242and 6,534,261, incorporated by reference herein in their entireties.

Exemplary selection methods, including phage display and two-hybridsystems, are disclosed in U.S. Pat. Nos. 5,789,538; 5,925,523;6,007,988; 6,013,453; 6,410,248; 6,140,466; 6,200,759; and 6,242,568; aswell as WO 98/37186; WO 98/53057; WO 00/27878; WO 01/88197 and GB2,338,237. In addition, enhancement of binding specificity for zincfinger binding domains has been described, for example, in co-owned WO02/077227.

In addition, as disclosed in these and other references, zinc fingerdomains and/or multi-fingered zinc finger proteins may be linkedtogether using any suitable linker sequences, including for example,linkers of 5 or more amino acids in length. See, also, U.S. Pat. Nos.6,479,626; 6,903,185; and 7,153,949 for exemplary linker sequences 6 ormore amino acids in length. The proteins described herein may includeany combination of suitable linkers between the individual zinc fingersof the protein.

In some aspects, the DNA-binding domain targets an IL2RG or RAG gene. Incertain embodiments, the DNA-binding domain targets an intronic regionof IL2RG or a RAG gene, for example intron 1 or intron 2.

Selection of target sites (e.g., within an intronic region of IL2RG or aRAG gene); ZFPs and methods for design and construction of fusionproteins (and polynucleotides encoding same) are known to those of skillin the art and described in detail in U.S. Pat. Nos. 6,140,081;5,789,538; 6,453,242; 6,534,261; 5,925,523; 6,007,988; 6,013,453;6,200,759; WO 95/19431; WO 96/06166; WO 98/53057; WO 98/54311; WO00/27878; WO 01/60970 WO 01/88197; WO 02/099084; WO 98/53058; WO98/53059; WO 98/53060; WO 02/016536 and WO 03/016496.

In addition, as disclosed in these and other references, zinc fingerdomains and/or multi-fingered zinc finger proteins may be linkedtogether using any suitable linker sequences, including for example,linkers of 5 or more amino acids in length. See, also, U.S. Pat. Nos.6,479,626; 6,903,185; and 7,153,949 for exemplary linker sequences 6 ormore amino acids in length. The proteins described herein may includeany combination of suitable linkers between the individual zinc fingersof the protein.

In certain embodiments, the DNA-binding molecule is part of a CRISPR/Casnuclease system. See, e.g., U.S. Pat. No. 8,697,359 and U.S. PatentPublication No, 20150056705. The CRISPR (clustered regularly interspacedshort palindromic repeats) locus, which encodes RNA components of thesystem, and the cas (CRISPR-associated) locus, which encodes proteins(Jansen et al., 2002. Mol. Microbial. 43: 1565-1575; Makarova et al.,2002. Nucleic Acids Res. 30: 482-496; Makarova et al., 2006. Biol.Direct 1: 7; Haft et al., 2005. PLoS Comput. Biol. 1: e60) make up thegene sequences of the CRISPR/Cas nuclease system. CRISPR loci inmicrobial hosts contain a combination of CRISPR-associated (Cas) genesas well as non-coding RNA elements capable of programming thespecificity of the CRISPR-mediated nucleic acid cleavage.

The Type II CRISPR is one of the most well characterized systems andcarries out targeted DNA double-strand break in four sequential steps.First, two non-coding RNA, the pre-crRNA array and tracrRNA, aretranscribed from the CRISPR locus. Second, tracrRNA hybridizes to therepeat regions of the pre-crRNA and mediates the processing of pre-crRNAinto mature crRNAs containing individual spacer sequences. Third, themature crRNA:tracrRNA complex directs Cas9 to the target DNA viaWatson-Crick base-pairing between the spacer on the crRNA and theprotospacer on the target DNA next to the protospacer adjacent motif(PAM), an additional requirement for target recognition. Finally, Cas9mediates cleavage of target DNA to create a double-stranded break withinthe protospacer. Activity of the CRISPR/Cas system comprises of threesteps: (i) insertion of alien DNA sequences into the CRISPR array toprevent future attacks, in a process called ‘adaptation’, (ii)expression of the relevant proteins, as well as expression andprocessing of the array, followed by (iii) RNA-mediated interferencewith the alien nucleic acid. Thus, in the bacterial cell, several of theso-called ‘Cas’ proteins are involved with the natural function of theCRISPR/Cas system and serve roles in functions such as insertion of thealien DNA etc.

In certain embodiments, Cas protein may be a “functional derivative” ofa naturally occurring Cas protein. A “functional derivative” of a nativesequence polypeptide is a compound having a qualitative biologicalproperty in common with a native sequence polypeptide. “Functionalderivatives” include, but are not limited to, fragments of a nativesequence and derivatives of a native sequence polypeptide and itsfragments, provided that they have a biological activity in common witha corresponding native sequence polypeptide. A biological activitycontemplated herein is the ability of the functional derivative tohydrolyze a DNA substrate into fragments. The term “derivative”encompasses both amino acid sequence variants of polypeptide, covalentmodifications, and fusions thereof. Suitable derivatives of a Caspolypeptide or a fragment thereof include but are not limited tomutants, fusions, covalent modifications of Cas protein or a fragmentthereof. Cas protein, which includes Cas protein or a fragment thereof,as well as derivatives of Cas protein or a fragment thereof, may beobtainable from a cell or synthesized chemically or by a combination ofthese two procedures. The cell may be a cell that naturally produces Casprotein, or a cell that naturally produces Cas protein and isgenetically engineered to produce the endogenous Cas protein at a higherexpression level or to produce a Cas protein from an exogenouslyintroduced nucleic acid, which nucleic acid encodes a Cas that is sameor different from the endogenous Cas. In some case, the cell does notnaturally produce Cas protein and is genetically engineered to produce aCas protein. In some embodiments, the Cas protein is a small Cas9ortholog for delivery via an AAV vector (Ran et at (2015) Nature 510, p.186).

In some embodiments, the DNA binding molecule is part of a TtAgo system(see Swarts et al, ibid; Sheng et al, ibid). In eukaryotes, genesilencing is mediated by the Argonaute (Ago) family of proteins. In thisparadigm, Ago is bound to small (19-31 nt) RNAs. This protein-RNAsilencing complex recognizes target RNAs via Watson-Crick base pairingbetween the small RNA and the target and endonucleolytically cleaves thetarget RNA (Vogel (2014) Science 344:972-973). In contrast, prokaryoticAgo proteins bind to small single-stranded DNA fragments and likelyfunction to detect and remove foreign (often viral) DNA (Yuan et al.,(2005) Mol. Cell 19, 405; Olovnikov, et al. (2013) Mol. Cell 51, 594;Swarts et al., ibid). Exemplary prokaryotic Ago proteins include thosefrom Aquifex aeolicus, Rhodobacter sphaeroides, and Thermusthermophilus.

One of the most well-characterized prokaryotic Ago protein is the onefrom T. thermophilus (TtAgo; Swarts et al. ibid). TtAgo associates witheither 15 nt or 13-25 nt single-stranded DNA fragments with 5′ phosphategroups. This “guide DNA” bound by TtAgo serves to direct the protein-DNAcomplex to bind a Watson-Crick complementary DNA sequence in athird-party molecule of DNA. Once the sequence information in theseguide DNAs has allowed identification of the target DNA, the TtAgo-guideDNA complex cleaves the target DNA. Such a mechanism is also supportedby the structure of the TtAgo-guide DNA complex while bound to itstarget DNA (G. Sheng et al., ibid). Ago from Rhodobacter sphaeroides(RsAgo) has similar properties (Olivnikov et al. ibid).

Exogenous guide DNAs of arbitrary DNA sequence can be loaded onto theTtAgo protein (Swarts et al. ibid.). Since the specificity of TtAgocleavage is directed by the guide DNA, a TtAgo-DNA complex formed withan exogenous, investigator-specified guide DNA will therefore directTtAgo target DNA cleavage to a complementary investigator-specifiedtarget DNA. In this way, one may create a targeted double-strand breakin DNA. Use of the TtAgo-guide DNA system (or orthologous Ago-guide DNAsystems from other organisms) allows for targeted cleavage of genomicDNA within cells. Such cleavage can be either single- ordouble-stranded. For cleavage of mammalian genomic DNA, it would bepreferable to use of a version of TtAgo codon optimized for expressionin mammalian cells. Further, it might be preferable to treat cells witha TtAgo-DNA complex formed in vitro where the TtAgo protein is fused toa cell-penetrating peptide. Further, it might be preferable to use aversion of the TtAgo protein that has been altered via mutagenesis tohave improved activity at 37 degrees Celcius. Ago-RNA-mediated DNAcleavage could be used to effect a panopoly of outcomes including geneknock-out, targeted gene addition, gene correction, targeted genedeletion using techniques standard in the art for exploitation of DNAbreaks.

Thus, the nuclease comprises a DNA-binding molecule in that specificallybinds to a target site in any gene into which it is desired to insert adonor (transgene), particularly an IL2RG and/or Rag transgene.

B. Cleavage Domains

Any suitable cleavage domain can be operatively linked to a DNA-bindingdomain to form a nuclease. For example, ZFP DNA-binding domains havebeen fused to nuclease domains to create ZFNs—a functional entity thatis able to recognize its intended nucleic acid target through itsengineered (ZFP) DNA binding domain and cause the DNA to be cut near theZFP binding site via the nuclease activity, including for use in genomemodification in a variety of organisms. See, for example, U.S. Pat. Nos.7,888,121; 8,623,618; 7,888,121; 7,914,796; and 8,034,598 and U.S.Publication No. 20110201055. Likewise, TALE DNA-binding domains havebeen fused to nuclease domains to create TALENs. See, e.g., U.S. Pat.No. 8,586,526.

As noted above, the cleavage domain may be heterologous to theDNA-binding domain, for example a zinc finger DNA-binding domain and acleavage domain from a nuclease or a TALEN DNA-binding domain and acleavage domain, or meganuclease DNA-binding domain and cleavage domainfrom a different nuclease. Heterologous cleavage domains can be obtainedfrom any endonuclease or exonuclease. Exemplary endonucleases from whicha cleavage domain can be derived include, but are not limited to,restriction endonucleases and homing endonucleases. Additional enzymeswhich cleave DNA are known (e.g., S1 Nuclease; mung bean nuclease;pancreatic DNase I; micrococcal nuclease; yeast HO endonuclease. One ormore of these enzymes (or functional fragments thereof) can be used as asource of cleavage domains and cleavage half-domains.

Similarly, a cleavage half-domain can be derived from any nuclease orportion thereof, as set forth above, that requires dimerization forcleavage activity. In general, two fusion proteins are required forcleavage if the fusion proteins comprise cleavage half-domains.Alternatively, a single protein comprising two cleavage half-domains canbe used. The two cleavage half-domains can be derived from the sameendonuclease (or functional fragments thereof), or each cleavagehalf-domain can be derived from a different endonuclease (or functionalfragments thereof). In addition, the target sites for the two fusionproteins are preferably disposed, with respect to each other, such thatbinding of the two fusion proteins to their respective target sitesplaces the cleavage half-domains in a spatial orientation to each otherthat allows the cleavage half-domains to form a functional cleavagedomain, e.g., by dimerizing. Thus, in certain embodiments, the nearedges of the target sites are separated by 5-8 nucleotides or by 15-18nucleotides. However any integral number of nucleotides or nucleotidepairs can intervene between two target sites (e.g., from 2 to 50nucleotide pairs or more). In general, the site of cleavage lies betweenthe target sites.

Restriction endonucleases (restriction enzymes) are present in manyspecies and are capable of sequence-specific binding to DNA (at arecognition site), and cleaving DNA at or near the site of binding.Certain restriction enzymes (e.g., Type IIS) cleave DNA at sites removedfrom the recognition site and have separable binding and cleavagedomains. For example, the Type IIS enzyme Fok I catalyzesdouble-stranded cleavage of DNA, at 9 nucleotides from its recognitionsite on one strand and 13 nucleotides from its recognition site on theother. See, for example, U.S. Pat. Nos. 5,356,802; 5,436,150 and5,487,994; as well as Li et al. (1992) Proc. Natl. Acad. Sci. USA89:4275-4279; Li et al. (1993) Proc. Natl. Acad. Sci. USA 90:2764-2768;Kim et al. (1994a) Proc. Natl. Acad. Sci. USA 91:883-887; Kim et al.(1994b) J. Biol. Chem. 269:31,978-31,982. Thus, in one embodiment,fusion proteins comprise the cleavage domain (or cleavage half-domain)from at least one Type IIS restriction enzyme and one or more zincfinger binding domains, which may or may not be engineered.

An exemplary Type IIS restriction enzyme, whose cleavage domain isseparable from the binding domain, is Fok I. This particular enzyme isactive as a dimer. Bitinaite et al. (1998) Proc. Natl. Acad. Sci. USA95: 10,570-10,575. Accordingly, for the purposes of the presentdisclosure, the portion of the Fok I enzyme used in the disclosed fusionproteins is considered a cleavage half-domain. Thus, for targeteddouble-stranded cleavage and/or targeted replacement of cellularsequences using zinc finger-Fok I fusions, two fusion proteins, eachcomprising a FokI cleavage half-domain, can be used to reconstitute acatalytically active cleavage domain. Alternatively, a singlepolypeptide molecule containing a zinc finger binding domain and two FokI cleavage half-domains can also be used. Parameters for targetedcleavage and targeted sequence alteration using zinc finger-Fok Ifusions are provided elsewhere in this disclosure.

A cleavage domain or cleavage half-domain can be any portion of aprotein that retains cleavage activity, or that retains the ability tomultimerize (e.g., dimerize) to form a functional cleavage domain.

Exemplary Type IIS restriction enzymes are described in InternationalPublication WO 07/014275, incorporated herein in its entirety.Additional restriction enzymes also contain separable binding andcleavage domains, and these are contemplated by the present disclosure.See, for example, Roberts et al. (2003) Nucleic Acids Res. 31:418-420.

In certain embodiments, the cleavage domain comprises one or moreengineered cleavage half-domain (also referred to as dimerization domainmutants) that minimize or prevent homodimerization, as described, forexample, in U.S. Pat. Nos. 8,623,618; 7,888,121; 7,914,796; and8,034,598 and U.S. Publication No. 20110201055, the disclosures of allof which are incorporated by reference in their entireties herein. Aminoacid residues at positions 446, 447, 479, 483, 484, 486, 487, 490, 491,496, 498, 499, 500, 531, 534, 537, and 538 of FokI are all targets forinfluencing dimerization of the FokI cleavage half-domains.

Cleavage domains with more than one mutation may be used, for examplemutations at positions 490 (E→K) and 538 (I→K) in one cleavagehalf-domain to produce an engineered cleavage half-domain designated“E490K:I538K” and by mutating positions 486 (Q→E) and 499 (I→L) inanother cleavage half-domain to produce an engineered cleavagehalf-domain designated “Q486E:I499L;” mutations that replace the wildtype Gln (Q) residue at position 486 with a Glu (E) residue, the wildtype Iso (I) residue at position 499 with a Leu (L) residue and thewild-type Asn (N) residue at position 496 with an Asp (D) or Glu (E)residue (also referred to as a “ELD” and “ELE” domains, respectively);engineered cleavage half-domain comprising mutations at positions 490,538 and 537 (numbered relative to wild-type FokI), for instancemutations that replace the wild type Glu (E) residue at position 490with a Lys (K) residue, the wild type Iso (I) residue at position 538with a Lys (K) residue, and the wild-type His (H) residue at position537 with a Lys (K) residue or a Arg (R) residue (also referred to as“KKK” and “KKR” domains, respectively); and/or engineered cleavagehalf-domain comprises mutations at positions 490 and 537 (numberedrelative to wild-type FokI), for instance mutations that replace thewild type Glu (E) residue at position 490 with a Lys (K) residue and thewild-type His (H) residue at position 537 with a Lys (K) residue or aArg (R) residue (also referred to as “KIK” and “KIR” domains,respectively). See, e.g., U.S. Pat. Nos. 7,914,796; 8,034,598 and8,623,618, the disclosures of which are incorporated by reference in itsentirety for all purposes. In other embodiments, the engineered cleavagehalf domain comprises the “Sharkey” and/or “Sharkey′” mutations (see Guoet al, (2010) J. Mol. Biol. 400(1):96-107).

Alternatively, nucleases may be assembled in vivo at the nucleic acidtarget site using so-called “split-enzyme” technology (see, e.g. U.S.Patent Publication No. 20090068164). Components of such split enzymesmay be expressed either on separate expression constructs, or can belinked in one open reading frame where the individual components areseparated, for example, by a self-cleaving 2A peptide or IRES sequence.Components may be individual zinc finger binding domains or domains of ameganuclease nucleic acid binding domain.

Nucleases can be screened for activity prior to use, for example in ayeast-based chromosomal system as described in U.S. Pat. No. 8,563,314.

The Cas9 related CRISPR/Cas system comprises two RNA non-codingcomponents: tracrRNA and a pre-crRNA array containing nuclease guidesequences (spacers) interspaced by identical direct repeats (DRs). Touse a CRISPR/Cas system to accomplish genome engineering, both functionsof these RNAs must be present (see Cong et al, (2013) Sciencexpress1/10.1126/science 1231143). In some embodiments, the tracrRNA andpre-crRNAs are supplied via separate expression constructs or asseparate RNAs. In other embodiments, a chimeric RNA is constructed wherean engineered mature crRNA (conferring target specificity) is fused to atracrRNA (supplying interaction with the Cas9) to create a chimericcr-RNA-tracrRNA hybrid (also termed a single guide RNA). (see Jinek ibidand Cong, ibid).

Target Sites

As described in detail above, DNA-binding domains can be engineered tobind to any sequence of choice. An engineered DNA-binding domain canhave a novel binding specificity, compared to a naturally-occurringDNA-binding domain.

In certain embodiments, the nuclease(s) target(s) an IL2R2 gene or RAGgene (e.g., RAG1 or RAG2), for example an intron (e.g., intron 1 orintron 2) or an exon (e.g., exon 1) of the gene.

In certain embodiments, the nuclease target(s) a “safe harbor” loci suchas the AAVS1, HPRT, ALB and CCR5 genes in human cells, and Rosa26 inmurine cells (see, e.g., U.S. Pat. Nos. 7,888,121; 7,972,854; 7,914,796;7,951,925; 8,110,379; 8,409,861; 8,586,526; U.S. Patent Publications20030232410; 20050208489; 20050026157; 20060063231; 20080159996;201000218264; 20120017290; 20110265198; 20130137104; 20130122591;20130177983 and 20130177960) and the Zp15 locus in plants (see U.S. Pat.No. 8,329,986).

Addition non-limiting examples of suitable target genes include a beta(β) globin gene (HBB), a gamma (δ) globin gene (HBG1), a B-celllymphoma/leukemia 11A (BCL11A) gene, a Kruppel-like factor 1 (KLF1)gene, a CCR5 gene, a CXCR4 gene, a PPP1R12C (AAVS1) gene, anhypoxanthine phosphoribosyltransferase (HPRT) gene, an albumin gene, aFactor VIII gene, a Factor IX gene, a Leucine-rich repeat kinase 2(LRRK2) gene, a Hungtingin (Htt) gene, a rhodopsin (RHO) gene, a CysticFibrosis Transmembrane Conductance Regulator (CFTR) gene, a surfactantprotein B gene (SFTPB), a T-cell receptor alpha (TRAC) gene, a T-cellreceptor beta (TRBC) gene, a programmed cell death 1 (PD1) gene, aCytotoxic T-Lymphocyte Antigen 4 (CTLA-4) gene, an human leukocyteantigen (HLA) A gene, an HLA B gene, an HLA C gene, an HLA-DPA gene, anHLA-DQ gene, an HLA-DRA gene, a LMP7 gene, a Transporter associated withAntigen Processing (TAP) 1 gene, a TAP2 gene, a tapasin gene (TAPBP), aclass II major histocompatibility complex transactivator (CIITA) gene, adystrophin gene (DMD), a glucocorticoid receptor gene (GR), an IL2RGgene, a Rag-1 gene, an RFX5 gene, a FAD2 gene, a FAD3 gene, a ZP15 gene,a KASII gene, a MDH gene, and/or an EPSPS gene. In some aspects, thenuclease(s) binds to and/or cleaves a check point inhibitor gene, forexample PD-1, CTLA4, receptors for the B7 family of inhibitory ligands,or cleaves a receptor or ligand gene involved in signaling through LAG3,2B4, BTLA, TIM3, A2aR, and killer inhibitor receptors (KIRs and C-typelectin receptors), see Pardoll (2012) Nat Rev Cancer 12(4):252, an HLAcomplex gene (class I: HLA-A, HLA-B, HLA-C, HLA-E, HLA-F, HLA-G, B2M;class II: HLA-DMA, HLA-DOA, HLA-DPA1, HLA-DQA, HLA-DRA, HLA-DMB,HLA-DOB, HLA-DPB1, HLA-DQB, HLA-DRB) or TCR; and/or a gene encoding aproduct involved in the peptide loading process and antigen processingfor the HLA complexes (e.g. TAP, tapasin, calreticulin, calnexin, LMP2,LMP7 or Erp57). See, e.g., U.S. Pat. Nos. 8,956,828 and 8,945,868.

Donors

In certain embodiments, the present disclosure relates tonuclease-mediated targeted integration of an exogenous sequence encodingan IL2RG and/or Rag protein (e.g., any functional fragment of an IL2RGand/or Rag protein) into the genome of a cell. As noted above, insertionof an exogenous sequence (also called a “donor sequence” or “donor” or“transgene”), for example for deletion of a specified region and/orcorrection of a mutant gene or for increased expression of a wild-typegene. It will be readily apparent that the donor sequence is typicallynot identical to the genomic sequence where it is placed. A donorsequence can contain a non-homologous sequence (e.g., a transgene)flanked by two regions of homology to allow for efficient HDR at thelocation of interest or can be integrated via non-homology directedrepair mechanisms. See, e.g., U.S. Pat. Nos. 9,045,763; 9,005,973 and7,888,121. Additionally, donor sequences can comprise a vector moleculecontaining sequences that are not homologous to the region of interestin cellular chromatin. A donor molecule can contain several,discontinuous regions of homology to cellular DNA. Further, for targetedinsertion of sequences not normally present in a region of interest,said sequences can be present in a donor nucleic acid molecule andflanked by regions of homology to sequence in the region of interest.

As with nucleases, the donors can be introduced into any form. Incertain embodiments, the donors may be introduced using DNA and/or viralvectors by methods known in the art. See, e.g., U.S. Pat. Nos.9,005,973; 8,936,936 and 8,703,489. The donor may be introduced into thecell in double- or single-stranded form. The donor may be introducedinto the cell in circular or linear form. If introduced in linear form,the ends of the donor sequence can be protected (e.g., fromexonucleolytic degradation) by methods known to those of skill in theart. For example, one or more dideoxynucleotide residues are added tothe 3′ terminus of a linear molecule and/or self-complementaryoligonucleotides are ligated to one or both ends. See, for example,Chang et al. (1987) Proc. Natl. Acad. Sci. USA 84:4959-4963; Nehls etal. (1996) Science 272:886-889. Additional methods for protectingexogenous polynucleotides from degradation include, but are not limitedto, addition of terminal amino group(s) and the use of modifiedinternucleotide linkages such as, for example, phosphorothioates,phosphoramidates, and O-methyl ribose or deoxyribose residues.

In certain embodiments, the donor includes sequences (e.g., codingsequences, also referred to as transgenes) greater than 1 kb in length,for example between 2 and 200 kb, between 2 and 10 kb (or any valuetherebetween). The donor may also include at least one nuclease targetsite. In certain embodiments, the donor includes at least 2 targetsites, for example for a pair of ZFNs, TALENs, TtAgo or CRISPR/Casnucleases. Typically, the nuclease target sites are outside thetransgene sequences, for example, 5′ and/or 3′ to the transgenesequences, for cleavage of the transgene. The nuclease cleavage site(s)may be for any nuclease(s). In certain embodiments, the nuclease targetsite(s) contained in the double-stranded donor are for the samenuclease(s) used to cleave the endogenous target into which the cleaveddonor is integrated via homology-independent methods.

The donor can be inserted so that its expression is driven by theendogenous promoter at the integration site, namely the promoter thatdrives expression of the endogenous gene into which the donor isinserted. However, it will be apparent that the donor may comprise apromoter and/or enhancer, for example a constitutive promoter or aninducible or tissue specific promoter.

The donor molecule may be inserted into an endogenous gene such thatall, some or none of the endogenous gene is expressed. In someembodiments, the SCID-related (e.g., IL2RG and/or RAG) transgene isintegrated into the endogenous locus of the gene to correct a mutantversion (e.g., in a cell from a SCID patient that is lacking ordeficient in a functional version of the SCID-related gene). In certainembodiments, an IL2RG transgene is integrated into an endogenous IL2RGgene, for example an intronic region (e.g., intron 1) of a mutant IL2RGassociated with X-SCID. In certain embodiments, a RAG transgene (e.g.,RAG1 or RAG2) is integrated into an endogenous RAG gene, for example anintronic region (e.g., intron 1 or 2 of RAG1 and/or RAG2) of a mutantRAG associated with a form of SCID such as Omenn Syndrome. The donor mayinclude any SCID-related protein-encoding sequences that produce afunctional protein, including but not limited to full-lengthSCID-related genes (e.g., IL2RG, RAG1, and/or RAG2), partial(functional) sequences of SCID-related genes (e.g., exons 2-8 of IL2RG,exon 3 of RAG1 or RAG2, etc.) and combinations thereof. In otherembodiments, the SCID-related gene transgene is integrated into anyendogenous locus, for example a safe-harbor locus. See, e.g., U.S. Pat.Nos. 7,951,925; 8,110,379; and U.S. Patent Publication Nos. 2010218264;20130177983 and 20130196373.

Furthermore, although not required for expression, exogenous sequencesmay also include transcriptional or translational regulatory or othersequences, for example, promoters, enhancers, insulators, internalribosome entry sites, sequences encoding 2A peptides and/orpolyadenylation signals. Additionally, splice acceptor sequences may beincluded. Exemplary splice acceptor site sequences are known to those ofskill in the art and include, by way of example only,CTGACCTCTTCTCTTCCTCCCACAG, (SEQ ID NO:1) (from the human HBB gene) andTTTCTCTCCACAG (SEQ ID NO:2) (from the human Immunoglobulin-gamma gene).

The SCID-related transgenes carried on the donor sequences describedherein may be isolated from plasmids, cells or other sources usingstandard techniques known in the art such as PCR. Donors for use caninclude varying types of topology, including circular supercoiled,circular relaxed, linear and the like. Alternatively, they may bechemically synthesized using standard oligonucleotide synthesistechniques. In addition, donors may be methylated or lack methylation.Donors may be in the form of bacterial or yeast artificial chromosomes(BACs or YACs).

The donor polynucleotides described herein may include one or morenon-natural bases and/or backbones. In particular, insertion of a donormolecule with methylated cytosines may be carried out using the methodsdescribed herein to achieve a state of transcriptional quiescence in aregion of interest.

The exogenous (donor) polynucleotide may comprise any sequence ofinterest (exogenous sequence). Exemplary exogenous sequences include,but are not limited to any polypeptide coding sequence (e.g., cDNAs),promoter sequences, enhancer sequences, epitope tags, marker genes,cleavage enzyme recognition sites and various types of expressionconstructs. Marker genes include, but are not limited to, sequencesencoding proteins that mediate antibiotic resistance (e.g., ampicillinresistance, neomycin resistance, G418 resistance, puromycin resistance),sequences encoding colored or fluorescent or luminescent proteins (e.g.,green fluorescent protein, enhanced green fluorescent protein, redfluorescent protein, luciferase), and proteins which mediate enhancedcell growth and/or gene amplification (e.g., dihydrofolate reductase).Epitope tags include, for example, one or more copies of FLAG, His, myc,Tap, HA or any detectable amino acid sequence.

In some embodiments, the donor further comprises a polynucleotideencoding any polypeptide of which expression in the cell is desired,including, but not limited to antibodies, antigens, enzymes, receptors(cell surface or nuclear or chimeric antigen receptors (CARs)),hormones, lymphokines, cytokines, reporter polypeptides, growth factors,and functional fragments of any of the above. The coding sequences maybe, for example, cDNAs.

In certain embodiments, the exogenous sequences can comprise a markergene (described above), allowing selection of cells that have undergonetargeted integration, and a linked sequence encoding an additionalfunctionality. Non-limiting examples of marker genes include GFP, drugselection marker(s) and the like.

In certain embodiments, the transgene may include, for example,wild-type genes to replace mutated endogenous sequences. For example, awild-type (or other functional) IL2RG and/or RAG gene sequence may beinserted into the genome of a stem cell in which the endogenous copy ofthe gene is mutated. The transgene may be inserted at the endogenouslocus, or may alternatively be targeted to a safe harbor locus.

Construction of such expression cassettes, following the teachings ofthe present specification, utilizes methodologies well known in the artof molecular biology (see, for example, Ausubel or Maniatis). Before useof the expression cassette to generate a transgenic animal, theresponsiveness of the expression cassette to the stress-inducerassociated with selected control elements can be tested by introducingthe expression cassette into a suitable cell line (e.g., primary cells,transformed cells, or immortalized cell lines).

Furthermore, although not required for expression, exogenous sequencesmay also transcriptional or translational regulatory sequences, forexample, promoters, enhancers, insulators, internal ribosome entrysites, sequences encoding 2A peptides and/or polyadenylation signals.Further, the control elements of the genes of interest can be operablylinked to reporter genes to create chimeric genes (e.g., reporterexpression cassettes).

Targeted insertion of non-coding nucleic acid sequence may also beachieved. Sequences encoding antisense RNAs, RNAi, shRNAs and micro RNAs(miRNAs) may also be used for targeted insertions.

In additional embodiments, the donor nucleic acid may comprisenon-coding sequences that are specific target sites for additionalnuclease designs. Subsequently, additional nucleases may be expressed incells such that the original donor molecule is cleaved and modified byinsertion of another donor molecule of interest. In this way,reiterative integrations of donor molecules may be generated allowingfor trait stacking at a particular locus of interest or at a safe harborlocus.

Cells

Thus, provided herein are genetically modified cells comprising aSCID-related transgene, namely a transgene that expresses a functionalprotein lacking or deficient in a SCID in the cell, including cellsproduced by the methods described herein. The transgene is integrated ina targeted manner into the cell's genome using one or more nucleases. Incertain embodiments, the transgene is integrated into IL2RG, for examplea mutant IL2RG gene as found in X-SCID patients. In certain embodiments,the transgene is integrated into a RAG gene, for example a mutant RAG1and/or RAG2 gene as found in Omenn Syndrome patients. The transgene maybe integrated into any intronic or exonic region of IL2RG or a RAG gene,for example intron 1 or intron 2. In other embodiments, the transgene isintegrated into a safe harbor gene. Thus, provided herein aregenetically modified cells comprising a SCID-related transgene (thatexpresses a functional protein lacking or deficient in a SCID)integrated in intron 1 or intron 2 of a SCID-related gene as well ascells descended from these cells that include the genetic modification.

Unlike random integration, targeted integration ensures that thetransgene is integrated into a specified gene. The transgene may beintegrated anywhere in the target gene. In certain embodiments, thetransgene is integrated at or near the nuclease cleavage site, forexample, within 1-300 (or any value therebetween) base pairs upstream ordownstream of the site of cleavage, more preferably within 1-100 basepairs (or any value therebetween) of either side of the cleavage site,even more preferably within 1 to 50 base pairs (or any valuetherebetween) of either side of the cleavage site. In certainembodiments, the integrated sequence comprising the transgene does notinclude any vector sequences (e.g., viral vector sequences).

Any cell type can be genetically modified as described herein tocomprise an IL2RG transgene, including but not limited to cells and celllines. Other non-limiting examples of IL2RG-transgene containing cellsas described herein include T-cells (e.g., CD4+, CD3+, CD8+, etc.);dendritic cells; B-cells; autologous (e.g., patient-derived) orheterologous pluripotent, totipotent or multipotent stem cells (e.g.,CD34+ cells, induced pluripotent stem cells (iPSCs), embryonic stemcells or the like). In certain embodiments, the cells as describedherein are CD34+ cells derived from an X-SCID patient.

The SCID-related protein-expressing cells as described herein are usefulin treating and/or preventing SCID (e.g., X-SCID and/or Omenn Syndrome)in a subject with the disorder, for example, by ex vivo therapies. Thenuclease-modified cells can be expanded and then reintroduced into thepatient using standard techniques. See, e.g., Tebas et at (2014) New EngJ Med 370(10):901. In the case of stem cells, after infusion into thesubject, in vivo differentiation of these precursors into cellsexpressing the functional IL2RG protein also occurs. Pharmaceuticalcompositions comprising the cells as described herein are also provided.In addition, the cells may be cryopreserved prior to administration to apatient.

The cells and ex vivo methods as described herein provide treatmentand/or prevention of SCID in a subject and eliminate the need forcontinuous prophylactic pharmaceutical administration or riskyprocedures such as allogeneic bone marrow transplants or gammaretroviral delivery. As such, the invention described herein provides asafer, cost-effective and time efficient way of treating and/orpreventing SCID.

Delivery

The nucleases, polynucleotides encoding these nucleases, donorpolynucleotides and compositions comprising the proteins and/orpolynucleotides described herein may be delivered by any suitable means.In certain embodiments, the nucleases and/or donors are delivered invivo. In other embodiments, the nucleases and/or donors are delivered toisolated cells (e.g., autologous or heterologous stem cells) for theprovision of modified cells useful in ex vivo delivery to SCID patients.

Methods of delivering nucleases as described herein are described, forexample, in U.S. Pat. Nos. 6,453,242; 6,503,717; 6,534,261; 6,599,692;6,607,882; 6,689,558; 6,824,978; 6,933,113; 6,979,539; 7,013,219; and7,163,824, the disclosures of all of which are incorporated by referenceherein in their entireties.

Nucleases and/or donor constructs as described herein may also bedelivered using any nucleic acid delivery mechanism, including naked DNAand/or RNA mRNA) and vectors containing sequences encoding one or moreof the components, Any vector systems may be used including, but notlimited to, plasmid vectors, DNA minicircles, retroviral vectors,lentiviral vectors, adenovirus vectors, poxvirus vectors; herpesvirusvectors and adeno-associated virus vectors, etc., and combinationsthereof. See, also, U.S. Pat. Nos. 6,534,261; 6,607,882; 6,824,978;6,933,113; 6,979,539; 7,013,219; and 7,163,824, and U.S. PatentPublication No. 20140335063, incorporated by reference herein in theirentireties. Furthermore, it will be apparent that any of these systemsmay comprise one or more of the sequences needed for treatment. Thus,when one or more nucleases and a donor construct are introduced into thecell, the nucleases and/or donor polynucleotide may be carried on thesame delivery system or on different delivery mechanisms. When multiplesystems are used, each delivery mechanism may comprise a sequenceencoding one or multiple nucleases and/or donor constructs (e.g., mRNAencoding one or more nucleases and/or mRNA or AAV carrying one or moredonor constructs).

Conventional viral and non-viral based gene transfer methods can be usedto introduce nucleic acids encoding nucleases and donor constructs incells (e.g., mammalian cells) and target tissues. Non-viral vectordelivery systems include DNA plasmids, DNA minicircles, naked nucleicacid, and nucleic acid complexed with a delivery vehicle such as aliposome or poloxamer. Viral vector delivery systems include DNA and RNAviruses, which have either episomal or integrated genomes after deliveryto the cell. For a review of gene therapy procedures, see Anderson,Science 256:808-813 (1992); Nabel & Felgner, TIBTECH 11:211-217 (1993);Mitani & Caskey, TIBTECH 11:162-166 (1993); Dillon, TIBTECH 11:167-175(1993); Miller, Nature 357:455-460 (1992); Van Brunt, Biotechnology6(10):1149-1154 (1988); Vigne, Restorative Neurology and Neuroscience8:35-36 (1995); Kremer & Perricaudet, British Medical Bulletin51(1):31-44 (1995); Haddada et al., in Current Topics in Microbiologyand Immunology Doerfler and Böhm (eds.) (1995); and Yu et al., GeneTherapy 1:13-26 (1994).

Methods of non-viral delivery of nucleic acids include electroporation,lipofection, microinjection, biolistics, virosomes, liposomes,immunoliposomes, polycation or lipid:nucleic acid conjugates, lipidnanoparticles (LNP), naked DNA, naked RNA, capped RNA, artificialvirions, and agent-enhanced uptake of DNA. Sonoporation using, e.g., theSonitron 2000 system (Rich-Mar) can also be used for delivery of nucleicacids.

Additional exemplary nucleic acid delivery systems include thoseprovided by Amaxa Biosystems (Cologne, Germany), Maxcyte, Inc.(Rockville, Md.), BTX Molecular Delivery Systems (Holliston, Mass.) andCopernicus Therapeutics Inc. (see for example U.S. Pat. No. 6,008,336).Lipofection is described in e.g., U.S. Pat. Nos. 5,049,386; 4,946,787;and 4,897,355) and lipofection reagents are sold commercially (e.g.,Transfectam™ and Lipofectin™). Cationic and neutral lipids that aresuitable for efficient receptor-recognition lipofection ofpolynucleotides include those of Felgner, WO 91/17424, WO 91/16024. Insome aspects, the nucleases are delivered as mRNAs and the transgene isdelivered via other modalities such as viral vectors, minicircle DNA,plasmid DNA, single-stranded DNA, linear DNA, liposomes, nanoparticlesand the like.

The preparation of lipid:nucleic acid complexes, including targetedliposomes such as immunolipid complexes, is well known to one of skillin the art (see, e.g., Crystal, Science 270:404-410 (1995); Blaese etal., Cancer Gene Ther. 2:291-297 (1995); Behr et al., Bioconjugate Chem.5:382-389 (1994); Remy et al., Bioconjugate Chem. 5:647-654 (1994); Gaoet al., Gene Therapy 2:710-722 (1995); Ahmad et al., Cancer Res.52:4817-4820 (1992); U.S. Pat. Nos. 4,186,183, 4,217,344, 4,235,871,4,261,975, 4,485,054, 4,501,728, 4,774,085, 4,837,028, and 4,946,787).

Additional methods of delivery include the use of packaging the nucleicacids to be delivered into EnGeneIC delivery vehicles (EDVs). These EDVsare specifically delivered to target tissues using bispecific antibodieswhere one arm of the antibody has specificity for the target tissue andthe other has specificity for the EDV. The antibody brings the EDVs tothe target cell surface and then the EDV is brought into the cell byendocytosis. Once in the cell, the contents are released (see MacDiarmidet at (2009) Nature Biotechnology 27(7):643).

The use of RNA or DNA viral based systems for the delivery of nucleicacids encoding engineered CRISPR/Cas systems take advantage of highlyevolved processes for targeting a virus to specific cells in the bodyand trafficking the viral payload to the nucleus. Viral vectors can beadministered directly to subjects (in vivo) or they can be used to treatcells in vitro and the modified cells are administered to subjects (exvivo). Conventional viral based systems for the delivery of CRISPR/Cassystems include, but are not limited to, retroviral, lentivirus,adenoviral, adeno-associated, vaccinia and herpes simplex virus vectorsfor gene transfer. Integration in the host genome is possible with theretrovirus, lentivirus, and adeno-associated virus gene transfermethods, often resulting in long term expression of the insertedtransgene. Additionally, high transduction efficiencies have beenobserved in many different cell types and target tissues.

The tropism of a retrovirus can be altered by incorporating foreignenvelope proteins, expanding the potential target population of targetcells. Lentiviral vectors are retroviral vectors that are able totransduce or infect non-dividing cells and typically produce high viraltiters. Selection of a retroviral gene transfer system depends on thetarget tissue. Retroviral vectors are comprised of cis-acting longterminal repeats with packaging capacity for up to 6-10 kb of foreignsequence. The minimum cis-acting LTRs are sufficient for replication andpackaging of the vectors, which are then used to integrate thetherapeutic gene into the target cell to provide permanent transgeneexpression. Widely used retroviral vectors include those based uponmurine leukemia virus (MuLV), gibbon ape leukemia virus (GaLV), SimianImmunodeficiency virus (SIV), human immunodeficiency virus (HIV), andcombinations thereof (see, e.g., Buchscher et al., J. Virol.66:2731-2739 (1992); Johann et al., J. Virol. 66:1635-1640 (1992);Sommerfelt et al., Virol. 176:58-59 (1990); Wilson et al., J. Virol.63:2374-2378 (1989); Miller et al., J. Virol. 65:2220-2224 (1991);PCT/US94/05700).

In applications in which transient expression is preferred, adenoviralbased systems can be used. Adenoviral based vectors are capable of veryhigh transduction efficiency in many cell types and do not require celldivision. With such vectors, high titer and high levels of expressionhave been obtained. This vector can be produced in large quantities in arelatively simple system. Adeno-associated virus (“AAV”) vectors arealso used to transduce cells with target nucleic acids, e.g., in the invitro production of nucleic acids and peptides, and for in vivo and exvivo gene therapy procedures (see, e.g., West et al., Virology 160:38-47(1987); U.S. Pat. No. 4,797,368; WO 93/24641; Kotin, Human Gene Therapy5:793-801 (1994); Muzyczka, J. Clin. Invest. 94:1351 (1994).Construction of recombinant AAV vectors are described in a number ofpublications, including U.S. Pat. No. 5,173,414; Tratschin et al., Mol.Cell. Biol. 5:3251-3260 (1985); Tratschin, et al., Mol. Cell. Biol.4:2072-2081 (1984); Hermonat & Muzyczka, PNAS 81:6466-6470 (1984); andSamulski et al., J. Virol. 63:03822-3828 (1989). Any AAV serotype can beused, including AAV1, AAV3, AAV4, AAV5, AAV6 and AAV8, AAV 8.2, AAV9,and AAV rh10 and pseudotyped AAV such as AAV2/8, AAV2/5 and AAV2/6.

At least six viral vector approaches are currently available for genetransfer in clinical trials, which utilize approaches that involvecomplementation of defective vectors by genes inserted into helper celllines to generate the transducing agent.

pLASN and MFG-S are examples of retroviral vectors that have been usedin clinical trials (Dunbar et al., Blood 85:3048-305 (1995); Kohn etal., Nat. Med. 1:1017-102 (1995); Malech et al., PNAS 94:22 12133-12138(1997)). PA317/pLASN was the first therapeutic vector used in a genetherapy trial. (Blaese et al., Science 270:475-480 (1995)). Transductionefficiencies of 50% or greater have been observed for MFG-S packagedvectors. (Ellem et al., Immunol Immunother. 44(1):10-20 (1997); Dranoffet al., Hum. Gene Ther. 1:111-2 (1997).

Recombinant adeno-associated virus vectors (rAAV) are a promisingalternative gene delivery systems based on the defective andnonpathogenic parvovirus adeno-associated type 2 virus. All vectors arederived from a plasmid that retains only the AAV 145 base pair (bp)inverted terminal repeats flanking the transgene expression cassette.Efficient gene transfer and stable transgene delivery due to integrationinto the genomes of the transduced cell are key features for this vectorsystem. (Wagner et al., Lancet 351:9117 1702-3 (1998), Kearns et al.,Gene Ther. 9:748-55 (1996)). Other AAV serotypes, including AAV1, AAV3,AAV4, AAV5, AAV6, AAV8, AAV9 and AAVrh10, and all variants thereof, canalso be used in accordance with the present invention.

Replication-deficient recombinant adenoviral vectors (Ad) can beproduced at high titer and readily infect a number of different celltypes. Most adenovirus vectors are engineered such that a transgenereplaces the Ad E1a, E1b, and/or E3 genes; subsequently the replicationdefective vector is propagated in human 293 cells that supply deletedgene function in trans. Ad vectors can transduce multiple types oftissues in vivo, including non-dividing, differentiated cells such asthose found in liver, kidney and muscle. Conventional Ad vectors have alarge carrying capacity. An example of the use of an Ad vector in aclinical trial involved polynucleotide therapy for anti-tumorimmunization with intramuscular injection (Sterman et al., Hum. GeneTher. 7:1083-9 (1998)). Additional examples of the use of adenovirusvectors for gene transfer in clinical trials include Rosenecker et al.,Infection 24:1 5-10 (1996); Sterman et al., Hum. Gene Ther. 9:71083-1089 (1998); Welsh et al., Hum. Gene Ther. 2:205-18 (1995); Alvarezet al., Hum. Gene Ther. 5:597-613 (1997); Topf et al., Gene Ther.5:507-513 (1998); Sterman et al., Hum. Gene Ther. 7:1083-1089 (1998).

Packaging cells are used to form virus particles that are capable ofinfecting a host cell. Such cells include 293 cells, which packageadenovirus, and ψ2 cells or PA317 cells, which package retrovirus. Viralvectors used in gene therapy are usually generated by a producer cellline that packages a nucleic acid vector into a viral particle. Thevectors typically contain the minimal viral sequences required forpackaging and subsequent integration into a host (if applicable), otherviral sequences being replaced by an expression cassette encoding theprotein to be expressed. The missing viral functions are supplied intrans by the packaging cell line. For example, AAV vectors used in genetherapy typically only possess inverted terminal repeat (ITR) sequencesfrom the AAV genome which are required for packaging and integrationinto the host genome. Viral DNA is packaged in a cell line, whichcontains a helper plasmid encoding the other AAV genes, namely rep andcap, but lacking ITR sequences. The cell line is also infected withadenovirus as a helper. The helper virus promotes replication of the AAVvector and expression of AAV genes from the helper plasmid. The helperplasmid is not packaged in significant amounts due to a lack of ITRsequences. Contamination with adenovirus can be reduced by, e.g., heattreatment to which adenovirus is more sensitive than AAV.

In many gene therapy applications, it is desirable that the gene therapyvector be delivered with a high degree of specificity to a particulartissue type. Accordingly, a viral vector can be modified to havespecificity for a given cell type by expressing a ligand as a fusionprotein with a viral coat protein on the outer surface of the virus. Theligand is chosen to have affinity for a receptor known to be present onthe cell type of interest. For example, Han et al., Proc. Natl. Acad.Sci. USA 92:9747-9751 (1995), reported that Moloney murine leukemiavirus can be modified to express human heregulin fused to gp70, and therecombinant virus infects certain human breast cancer cells expressinghuman epidermal growth factor receptor. This principle can be extendedto other virus-target cell pairs, in which the target cell expresses areceptor and the virus expresses a fusion protein comprising a ligandfor the cell-surface receptor. For example, filamentous phage can beengineered to display antibody fragments (e.g., FAB or Fv) havingspecific binding affinity for virtually any chosen cellular receptor.Although the above description applies primarily to viral vectors, thesame principles can be applied to nonviral vectors. Such vectors can beengineered to contain specific uptake sequences which favor uptake byspecific target cells.

Gene therapy vectors can be delivered in vivo by administration to anindividual subject, typically by systemic administration (e.g.,intravenous, intraperitoneal, intramuscular, subdermal, sublingual orintracranial infusion) topical application, as described below, or viapulmonary inhalation. Alternatively, vectors can be delivered to cellsex vivo, such as cells explanted from an individual patient (e.g.,lymphocytes, bone marrow aspirates, tissue biopsy) or universal donorhematopoietic stem cells, followed by reimplantation of the cells into apatient, usually after selection for cells which have incorporated thevector.

Vectors (e.g., retroviruses, adenoviruses, liposomes, etc.) containingnucleases and/or donor constructs can also be administered directly toan organism for transduction of cells in vivo. Alternatively, naked DNAcan be administered. Administration is by any of the routes normallyused for introducing a molecule into ultimate contact with blood ortissue cells including, but not limited to, injection, infusion, topicalapplication, inhalation and electroporation. Suitable methods ofadministering such nucleic acids are available and well known to thoseof skill in the art, and, although more than one route can be used toadminister a particular composition, a particular route can oftenprovide a more immediate and more effective reaction than another route.

Vectors suitable for introduction of polynucleotides described hereininclude non-integrating lentivirus vectors (IDLV). See, for example, Oryet al. (1996) Proc. Natl. Acad. Sci. USA 93:11382-11388; Dull et al.(1998) J. Virol. 72:8463-8471; Zuffery et al. (1998) J. Virol.72:9873-9880; Follenzi et al. (2000) Nature Genetics 25:217-222; U.S.Pat. No. 8,936,936.

Pharmaceutically acceptable carriers are determined in part by theparticular composition being administered, as well as by the particularmethod used to administer the composition. Accordingly, there is a widevariety of suitable formulations of pharmaceutical compositionsavailable, as described below (see, e.g., Remington's PharmaceuticalSciences, 17th ed., 1989).

It will be apparent that the nuclease-encoding sequences and donorconstructs can be delivered using the same or different systems. Forexample, a donor polynucleotide can be carried by an AAV, while the oneor more nucleases can be carried by mRNA. Furthermore, the differentsystems can be administered by the same or different routes(intramuscular injection, tail vein injection, other intravenousinjection, intraperitoneal administration and/or intramuscularinjection. Multiple vectors can be delivered simultaneously or in anysequential order.

Formulations for both ex vivo and in vivo administrations includesuspensions in liquid or emulsified liquids. The active ingredientsoften are mixed with excipients which are pharmaceutically acceptableand compatible with the active ingredient. Suitable excipients include,for example, water, saline, dextrose, glycerol, ethanol or the like, andcombinations thereof. In addition, the composition may contain minoramounts of auxiliary substances, such as, wetting or emulsifying agents,pH buffering agents, stabilizing agents or other reagents that enhancethe effectiveness of the pharmaceutical composition.

Applications

The methods and compositions disclosed herein are for providingtherapies for SCID, for example via the provision of proteins lacking ordeficient in a SCID disorder. The cell may be modified in vivo or may bemodified ex vivo and subsequently administered to a subject. Thus, themethods and compositions provide for the treatment and/or prevention ofa SCID disorder.

Targeted integration of an SCID-related transgene (e.g., IL2RG and/orRAG transgene) may be used to correct an aberrant SCID-related gene,insert a wild type gene, or change the expression of an endogenous gene.For instance, a wild-type transgene encoding IL2RG, which is deficientin X-SCID patients, may be integrated into a cell to provide a cell thatproduces a functional protein. Similarly, a wild-type transgene encodinga RAG gene (e.g., RAG1 or RAG2), which is deficient in Omenn SyndromeSCID patients, may be integrated into a cell to provide a cell thatproduces a functional Rag protein. Genomic editing may also includecorrection of mutations (e.g., point mutations) in a faulty endogenousgene, thereby resorting expression of the gene and treating thedisorder.

By way of non-limiting example, the methods and compositions describedherein can be used for treatment and/or prevention of SCID.

The following Examples relate to exemplary embodiments of the presentdisclosure in which the nuclease comprises a zinc finger nuclease (ZFN)or TALEN. It will be appreciated that this is for purposes ofexemplification only and that other nucleases can be used, for exampleTtAgo and CRISPR/Cas systems, homing endonucleases (meganucleases) withengineered DNA-binding domains and/or fusions of naturally occurring ofengineered homing endonucleases (meganucleases) DNA-binding domains andheterologous cleavage domains and/or fusions of meganucleases and TALEproteins.

EXAMPLES Example 1 Zinc Finger Protein Nucleases (ZFN) andTALE-Nucleases (TALENs) and Guide RNAs Targeted to IL2RG or RAG

Zinc finger proteins targeted to IL2RG or RAG1 were designed andincorporated into mRNA, plasmids, AAV or adenoviral vectors essentiallyas described in Urnov et al. (2005) Nature 435(7042):646-651, Perez etat (2008) Nature Biotechnology 26(7):808-816, and as described in U.S.Pat. No. 6,534,261. Table 1 shows the recognition helices within the DNAbinding domain of exemplary IL2RG or RAG1 ZFPs while Table 2 shows thetarget sites for these ZFPs (DNA target sites indicated in uppercaseletters; non-contacted nucleotides indicated in lowercase). Nucleotidesin the target site that are contacted by the ZFP recognition helices areindicated in uppercase letters; non-contacted nucleotides indicated inlowercase.

TABLE 1 Zinc finger proteins recognition helix designs Design SBS # F1F2 F3 F4 F5 F6 IL2RG-specific designs 41511 WRSCRSA DRSALSR QSGSLTRDRSHLTR RLDWLPM NA (SEQ ID (SEQ ID (SEQ ID (SEQ ID (SEQ ID NO: 3) NO: 4)NO: 5) NO: 6) NO: 7) 41512 QSGDLTR RRADLSR QRSNLDS RSANLAR QSANRTK NA(SEQ ID (SEQ ID (SEQ ID (SEQ ID (SEQ ID NO: 8) NO: 9) NO: 10) NO: 11)NO: 12) 41513 LRHHLTR LRHNLRA RSDALSR TSGNLTR RSDHLSA ESRYLMV (SEQ ID(SEQ ID (SEQ ID (SEQ ID (SEQ ID (SEQ ID NO: 13) NO: 14) NO: 15) NO: 16)NO: 17) NO: 18) 41514 QSGHLAR RKWTLQG RSDDLTR DRSTRRQ QSSDLSR QSGDLTR(SEQ ID (SEQ ID (SEQ ID (SEQ ID (SEQ ID (SEQ ID NO: 19) NO: 20) NO: 21)NO: 22) NO: 23) NO: 8) 41552 TSGNLTR QSNDLNS DRSHLTR QSGDLTR RSDSLLRQSYDRFQ (SEQ ID (SEQ ID (SEQ ID (SEQ ID (SEQ ID (SEQ ID NO: 16) NO: 24)NO: 6) NO: 8) NO: 25) NO: 26) 41553 QSGNLAR QSGDLTR RSDHLST RSDARTTDRSTRIT QNATRIN (SEQ ID (SEQ ID (SEQ ID (SEQ ID (SEQ ID (SEQ ID NO: 27)NO: 8) NO: 28) NO: 29) NO: 30) NO: 31) 41556 DRSHLTR QSGDLTR RSDSLLRQSYDRFQ RSDHLST QSANRTK (SEQ ID (SEQ ID (SEQ ID (SEQ ID (SEQ ID (SEQ IDNO: 6) NO: 8) NO: 25) NO: 26) NO: 28) NO: 12) 41558 RMYTLSK QSGNLARQSGDLTR RSDHLST RSDARTT NA (SEQ ID (SEQ ID (SEQ ID (SEQ ID (SEQ IDNO: 32) NO: 27) NO: 8) NO: 28) NO: 29) 41561 QSGDLTR RSDALAR ERGTLARRSDALTQ QSGALAR HKSARAA (SEQ ID (SEQ ID (SEQ ID (SEQ ID (SEQ ID (SEQ IDNO: 8) NO: 33) NO: 34) NO: 35) NO: 36) NO: 37) 41562 QSGHLAR LLHHLNNQSGNLAR WRISLAA RSDNLSA RSQNRTR (SEQ ID (SEQ ID (SEQ ID (SEQ ID (SEQ ID(SEQ ID NO: 19) NO: 38) NO: 27) NO: 39) NO: 40) NO: 41) 44271 TSGNLTRQSNDLNS YQGVLTR RSDNLRE RSDHLSQ TSANRTT (SEQ ID (SEQ ID (SEQ ID (SEQ ID(SEQ ID (SEQ ID NO: 16) NO: 24) NO: 42) NO: 43) NO: 44) NO: 45) 44298QSGNLAR QSGDLTR RSDHLSQ QSNGLTQ DRSTRIT QNATRIN (SEQ ID (SEQ ID (SEQ ID(SEQ ID (SEQ ID (SEQ ID NO: 27) NO: 8) NO: 44) NO: 46) NO: 30) NO: 31)RAG1-specific designs 54972 QRSNLVR TSGSLTR QGCNLGK DRSNLTR QSGDLTRWSTSLRA (SEQ ID (SEQ ID (SEQ ID (SEQ ID (SEQ ID (SEQ ID NO: 61) NO: 62)NO: 63) NO: 64) NO: 8) NO: 65) 50698 RSDSLLR WLSSLSA DRSNLSR HRQHLVTLRHHLTR DRSTLRQ (SEQ ID (SEQ ID (SEQ ID (SEQ ID (SEQ ID (SEQ ID NO: 25)NO: 66) NO: 67) NO: 68) NO: 13) NO: 69) 50718 QSSNLAR TSGSLTR QGCNLVKDRSNLTR QSGDLTR WSTSLRA (SEQ ID (SEQ ID (SEQ ID (SEQ ID (SEQ ID (SEQ IDNO: 70) NO: 62) NO: 71) NO: 64) NO: 8) NO: 65) 54950 RSDSLLR LRQNLVADRSNLSR HRQHLVT HRHHLGQ QNATRTK (SEQ ID (SEQ ID (SEQ ID (SEQ ID (SEQ ID(SEQ ID NO: 25) NO: 72) NO: 67) NO: 68) NO: 73) NO: 74) 55002 QSGNLARRHWSLSV QRTNLVE ASKTRTN RSDVLST STAALSY (SEQ ID (SEQ ID (SEQ ID (SEQ ID(SEQ ID (SEQ ID NO: 27) NO: 75) NO: 76) NO: 77) NO: 78) NO: 79) 50773NPANLTR QNATRTK QSSDLSR QLANLQT TSGNLTR N/A (SEQ ID (SEQ ID (SEQ ID(SEQ ID (SEQ ID NO: 97) NO: 74) NO: 23) NO: 80) NO: 16) 55005 QSGNLARRHWSLSV QRTNLVE ASKTRTN RSDVLST STAALSY (SEQ ID (SEQ ID (SEQ ID (SEQ ID(SEQ ID (SEQ ID NO: 27) NO: 75) NO: 76) NO: 77) NO: 78) NO: 79) 49812QSGNLAR RHWSLSV QRTNLVE ASKTRTN RSDVLST STAALSY (SEQ ID (SEQ ID (SEQ ID(SEQ ID (SEQ ID (SEQ ID NO: 27) NO: 75) NO: 76) NO: 77) NO: 78) NO: 79)

TABLE 2 Target Sites of zinc finger proteins SBS # Target siteIL2RG-specific target sites 41511 ccCTGGGTGTAGTCTGTctgtgtcagga(SEQ ID NO: 47) 41512 atGAAGAGCAAGCGCCAtgttgaagcca (SEQ ID NO: 48) 41513atAAGAGGGATGTGAATGGTaatgatgg (SEQ ID NO: 49) 41514ctGCAGCTgCCCCTGCTGGGAgtggggc (SEQ ID NO: 50) 41552ggCCAGTGGCAGGCaCCAGATctctgta (SEQ ID NO: 51) 41553ttACAATCATGTGGGCAGAAttgaaaag (SEQ ID NO: 52) 41556tgTAATGGCCAGTGGCAGGCaccagatc (SEQ ID NO: 53) 41558tcATGTGGGCAGAATTGaaaagtggagt (SEQ ID NO: 54) 41561tgATTGTAATGGCCaGTGGCAggcacca (SEQ ID NO: 55) 41562gtGGGCAGaATTGAAaAGTGGAgtggga (SEQ ID NO: 56) 44271gcCAGTGGCAGGCACCAGATctctgtac (SEQ ID NO: 57) 44298ttACAATCATGTGGGCAGAAttgaaaag (SEQ ID NO: 58) RAG1-specific target sites54972 tgTGTACAGACTAAGTTGAAgatgttan (SEQ ID NO: 81) 50698ttCCAAGTAATAACTGTGTGctcaagtg (SEQ ID NO: 82) 50718tgTGTACAGACTAAGTTGAAgatgttan (SEQ ID NO: 81) 54950ttCCAAGTAATAACTGTGTGctcaagtg (SEQ ID NO: 82) 55002ctTTTATGACCCATTTGGAAgaaataaa (SEQ ID NO: 83) 50773atGATAAAGCTGCAAACccaaagaaact (SEQ ID NO: 84) 55005ctTTTATGACCCATTTGGAAgaaataaa (SEQ ID NO: 83) 49812ctTTTATGACCCATTTGGAAgaaataaa (SEQ ID NO: 83)

All ZFN pairs were tested for cleavage activity and found to be active.Note that RAG1-specific ZFNs 55002, 55005 and 49812 all comprise thesame zinc finger helices, but have different linkers between zinc fingerhelix 4 and 5 contained within the DNA binding protein. ZFN 55002comprises a TGEKP linker (SEQ ID NO: 98), 55005 comprises a TGERG linker(SEQ ID NO: 99) and 49812 comprises a TGSQKP linker.

TALENs targeted to IL2RG were designed and incorporated into mRNA,plasmids, AAV or adenoviral vectors essentially as described in U.S.Pat. No. 8,586,526, including N-cap and/or C-cap sequences. The RVDs andtarget sites of the indicated exemplary TALENs are shown below in Tables3 and 4.

TABLE 3 IL2RG-specific TALE RVDs SBS# RVDs 102543NI-HD-NI-NN-NI-NN-NI-NG-HD-NG-NN-NN-NG- NN-HD-HD-NG 102544NG-HD-NG-NN-HD-HD-HD-NI-HD-NI-NG-NN-NI- NG-NG-NN-NG

TABLE 4 IL2RG-specific TALE Target Sites SBS# Target site 102543gtACAGAGATCTGGTGCCTgc (SEQ ID NO: 59) 102544atTCTGCCCACATGATTGTaa (SEQ ID NO: 60)

Specific CRISPR/Cas nucleases and guide RNAs are designed using methodsin the art. See e.g. U.S. Patent Publication No. 20150056705. Table 5shows exemplary guide RNAs (gRNAs) for use with S. pyogenes Cas9 fortargeting intron 1 of IL2RG, and introns 1 and 2 for RAG1 and RAG2.Sequences corresponding to the PAM sequence are shown in bold, and thelocation of the targeted sequence is shown as corresponds to the UCSCGRCh37/hg19 human genome assembly.

TABLE 5 Exemplary guide RNAs GRCh38.p2 Primary Gene LocusgRNA/PAM Sequence SEQ ID NO Assembly Location IL2RG Intron 1CACATGATTGTAATGGCCAGTGG 85 71111326-71111348 IL2RG Intron 1TTCTGCCCACATGATTGTAATGG 86 71111319-71111341 IL2RG Intron 1CACTGGCCATTACAATCATGTGG 87 71111347-71111325 RAG1 Intron 2TTGAGCACACAGTTATTACTTGG 88 36569004-36569026 RAG1 Intron 2TCTTCCAAATGGGTCATAAAAGG 89 36572801-36572779 RAG1 Intron 1CTECGCTCAAGGCIGGAGCTIGG 90 36565503-36565525 RAG1 Intron 1CCCAGACTAGTGATTAGCTGTGG 91 36565498-36565476 RAG2 Intron 2TCCCAGCTCCTTGGATGGAATGG 92 36594389-36594367 RAG2 Intron 2AACCGCTACCCTGGTATTGCTGG 93 36594713-36594735 RAG2 Intron 1TAATTCTGTAGTAAGTAAGCAGG 94 36595263-36595285 RAG2 Intron 1AATATACAACTGAGGGAGACAGG 95 36596442-36596420

The nucleases (ZFNs, CRISPR/Cas systems and TALENs) can includeengineered cleavage domains, in particular the heterodimers disclosed inU.S. Pat. No. 8,623,618 (e.g., ELD and KKR engineered cleavage domains).

Example 2 Activity of IL2RG-Targeted Nucleases

ZFNs and TALENs targeting intron 1 and exon 1 of the IL2RG gene (seeFIG. 1) were used to test the ability of these nucleases to cleave(e.g., induce DSBs) at a specific target site. In particular, the Cel-Imismatch assay (Surveyor™, Transgenomics; Perez et al, (2008) Nat.Biotechnol. 26: 808-816 and Guschin et al, (2010) Methods Mol Biol.649:247-56) was used where PCR-amplification of the target site wasfollowed by quantification of insertions and deletions (indels) usingthe mismatch detecting enzyme Cel-I (Yang et al, (2000) Biochemistry 39,3533-3541) which provides a lower-limit estimate of DSB frequency. Afterintroduction of the polynucleotides at standard conditions (37° C.) orcold-shock conditions (30° C.) (see, e.g., U.S. Pat. No. 8,772,008) intohuman K562 cells or CD34+ cells genomic DNA was isolated from the cellsusing the DNeasy™ kit (Qiagen).

The nucleases cleaved at their respective target sites as expected.Lanes are identified by the nuclease pair or control administered, andthe percent of PCR products wherein the nucleotides have been insertedand/or deleted (“indels”) are indicated at the bottom of each lane (“%NHEJ”). Exemplary results of gels are shown in FIGS. 2 and 3A. FIG. 3Band Table 6 below show high-throughput DNA sequencing analysis (%indels) of K562 cells containing the indicated exemplary ZFN pairs (topline) at day 3 and day 10 post-ZFN introduction. GFP (bottom line)served as a negative control. As shown, 44298:44271 ZFN pair yieldedhighest DNA cleaving activity.

TABLE 6 ZFN activity Day 3% Day 10% Day 3% Day 10% Day 3% Sample IndelsIndels Sample Indels Indels Sample Indels Day 10% Indels 44298:4427142.8 36.6 44330:44308 21.5 14.9 44364:44357 43.6 40.0Site3-Matrix-Day10-2 39.9 34.7 Site4-Matrix-Day10-9 21.2 14.2Site5-Matrix-Day10-2 40.1 37.0 Site3-Matrix-Day10-3 31.6Site4-Matrix-Day10-13 19.5 13.1 Site5-Matrix-Day10-6 40.8 36.9Site3-Matrix-Day10-13 34.8 28.4 Site4-Matrix-Day10-4 19.5 13.0Site5-Matrix-Day10-7 38.6 36.7 Site3-Matrix-Day10-6 32.5 28.1Site4-Matrix-Day10-16 21.9 12.9 Site5-Matrix-Day10-13 37.7 31.1Site3-Matrix-Day10-11 34.8 26.9 Site4-Matrix-Day10-8 20.0 12.6Site5-Matrix-Day10-1 35.9 31.0 Site3-Matrix-Day10-16 36.1 26.8Site4-Matrix-Day10-12 18.1 12.6 Site5-Matrix-Day10-8 34.5 30.3Site3-Matrix-Day10-1 26.8 25.3 Site4-Matrix-Day10-7 19.0 12.0Site5-Matrix-Day10-14 35.2 29.2 Site3-Matrix-Day10-9 30.6 24.8Site4-Matrix-Day10-11 18.1 11.5 Site5-Matrix-Day10-15 36.2 29.1Site3-Matrix-Day10-4 27.8 24.6 Site4-Matrix-Day10-1 19.9 11.4Site5-Matrix-Day10-10 32.4 28.2 Site3-Matrix-Day10-5 31.2 24.6Site4-Matrix-Day10-3 18.1 11.1 Site5-Matrix-Day10-9 33.3 28.1Site3-Matrix-Day10-15 32.5 24.3 Site4-Matrix-Day10-2 18.6 10.6Site5-Matrix-Day10-4 29.1 27.2 Site3-Matrix-Day10-10 26.8 24.2Site4-Matrix-Day10-15 18.4 10.3 Site5-Matrix-Day10-3 31.5 27.0Site3-Matrix-Day10-7 29.4 21.5 Site4-Matrix-Day10-10 17.2 9.7Site5-Matrix-Day10-11 31.2 26.9 Site 3 Parental 25.1 18.5Site4-Matrix-Day10-14 16.5 8.5 Site5-Matrix-Day10-12 28.1 25.5Site3-Matrix-Day10-12 22.3 16.7 Site 4 Parental 14.7 8.3Site5-Matrix-Day10-16 29.5 23.8 Site3-Matrix-Day10-8 22.3 15.1Site4-Matrix-Day10-6 13.0 8.2 Site 3 Parental 14.9 10.8 GFP 0.2 0.1 GFP0.2 0.1 GFP 0.2 0.1

Thus, the nucleases targeted to exon 1 and intron 1 of IL2RG were allcapable of cleaving the target gene.

Example 3 Methylcellulose Assay on Nuclease-Modified CD34+ Cells

Differentiation of the CD34+ cells as treated in Example 2 was analyzedby assay of colony types arising from Methocult-induced differentiation:colony-forming units, erythroid (“CFU-E”); burst-forming units,erythroid (“BFU-E”); colony-forming units, granulocyte/macrophage(“CFU-GM”) and colony-forming units;granulocyte/erythrocyte/monocyte/macrophage (“CFU-GEMM”) using standardmethodology as previously described (Genovese et al. (2014) Nature;510(7504):235-40). In short, CD34+ cells were genome modified, allowedto recover in vitro, then plated in methylcellulose medium and allowedto differentiate for 2 weeks before colonies were analyzed.

As shown in FIGS. 4A and 4B, the number of colonies formed fromdifferentiated CD34+ HSPCs was not significantly different betweengroups, however more granulocyte and monocyte forming units wereobserved in cell pools treated with 3 of the 6 nucleases compared to theGFP control.

Example 4 Targeted IL2RG Donor Insertion

A. Targeted Integration into IL2RG-Inactivated Jurkat Cell Lines

Targeted integration into the IL2RG locus was also performed. Exemplarydonor constructs for intron 1 of IL2RG (nucleases described inExample 1) are shown in FIG. 5. In particular, FIG. 5A shows an IL2RGgene with common mutations found in X-SCID patients. FIG. 5B shows anexemplary corrective partial cDNA donor with homology arms flanking thenuclease cleavage site in intron 1, a 5′ splice acceptor, andpolyadenylation signal tail to terminate transcription. FIG. 5C shows ananalogous intron 1 exemplary donor construct with a 2A-GFP construct toassay targeted integration and expression at the endogenous IL2RG locusvia flow cytometry or other fluorescence detection assays. FIG. 5D showsan illustration of insertion of the partial IL2RG donor construct intoIntron 1 of the IL2RG gene and subsequent production of a wild-typeprotein.

Jurkat clonal cell lines in which IL2RG was inactivated using ZFNstargeted to exon 5 of IL2RG (see, U.S. Pat. No. 7,888,121) were alsoprepared. Two clones were chosen for further experiments in which onehad a 17 base pair deletion in IL2RG (referred to as clone 2) and theother had a 1 base pair addition (referred to as clone 8). Bothmodifications yielded nonsense mutations and produced premature stopcodons in the coding sequence.

The nucleases (400 ng plasmid DNA/nuclease) and corrective IL2RG donorconstructs (1e6 vg/cell AAV6) as shown in FIG. 5 were introduced intoclonal cell lines 2 and 8. In short, the AAV6 donor was introduced tocells in RPMI medium, incubated at 37 C for 16 hours, cells were washed,then the nucleases were electroporated using an Amaxa SF kit. Total RNAwas harvested 3 days later. The donor were introduced as AAVs and thenucleases as DNA.

As shown in FIG. 6, IL2RG expression in cell lines with inactivated(exon 5) IL2RG were rescued by nuclease-mediated introduction of acorrective IL2RG transgene using nucleases targeted to intron 1 ofIL2RG. Significantly less IL2RG mRNA expression was seen in untreatedIL2RG knockouts as compared clones treated with AAV6 partial IL2RG cDNAdonor and either TALENs or ZFNs targeting intron 1 of IL2RG. Inaddition, high-throughput DNA sequencing analysis revealed that lessthan 5% targeted integration (TI) was sufficient to rescue the totallevel of IL2RG expression to endogenous levels.

B. Targeted Integration into CD34+ Cells

IL2RG nucleases in the form of mRNA were transfected into peripheralblood mobilized hematopoietic stem cells (CD34+ cells, from a maledonor, i.e. these cells only had one copy of the IL2RG gene per cell) orK562 cells. Briefly, 200,000 cells were transfected by BTXnucleofection. The concentrations of nucleases were 40 ug/mL mRNA eachper nucleofection. An AAV6 transgene donor (FIG. 5) was delivered 16hours prior to transfection. Integration of the exogenous DNA sequenceinto IL2RG was assayed by digestion of a PCR amplicon of the IL2RG locusfrom treated cells with the MluI restriction enzyme, by PCR usingprimers outside the donor region of homology, or by high-throughputsequencing (Miseq, Illumina).

As shown in FIGS. 7-10, targeted integration of the 6 bp RFLP sequencewas achieved in both CD34+ and K562 cells as determined by digestionwith the unique site introduced in the oligo donor.

As shown in FIGS. 11 and 12, targeted integration of a correctivepartial IL2RG cDNA donor were stably integrated into CD34+ cells asdetermined by the presence of a donor-specific restriction fragment(FIG. 11) and sequence analysis (FIG. 12). Furthermore, as shown in FIG.14, cells are viable following TI, cryopreservation and post-thawing ofcryopreserved cells.

Genomically edited (via TI) CD34+ cells were also evaluated fordifferentiation capability as described above in Example 3.

As shown in FIG. 13, no significant differences in lineagedifferentiation after nuclease or AAV modification was observed.Similarly, no difference in TI in erythroid versusgranulocyte/macrophage progenitor clones was observed.

C. Targeted Integration into Safe Harbor Loci

Corrective IL2RG donors may be integrated into safe harbor loci of CD34+cells, including HPRT, AAVS1, ALB, Rosa26, and/or CCR5 genes usingnucleases as described in U.S. Pat. Nos. 7,888,121; 7,972,854;7,914,796; 7,951,925; 8,110,379; 8,409,861; 8,586,526; U.S. PatentPublications 20030232410; 20050208489; 20050026157; 20060063231;20080159996; 201000218264; 20120017290; 20110265198; 20130137104;20130122591; 20130177983 and 20130177960 to produce functional IL2RG inthe cells.

Thus, the results demonstrate that nuclease-mediated stable targetedintegration of a corrective IL2RG transgene restored IL2RG expressionand that the modified cells maintained their differentiation potentialand viability following modification and/or cryopreservation.

Example 5 Targeted Integration into the RAG1 Gene

Targeted integration into the RAG1 locus was also performed usingexemplary RAG1-targeted ZFNs as shown in Table 1. A schematic of thegene is shown in FIG. 15, demonstrating the two splicing isoforms thatarise from this gene. FIG. 16 depicts exemplary donor constructscomprising a corrective cDNA donor with homology arms flanking thenuclease cleavage site in intron 2, a 5′ splice acceptor, andpolyadenylation signal tail to terminate transcription. Plasmid DNAencoding the ZFN pair 50773/49812, directed to Site 4 in RAG1 intron 2was introduced into K562 cells with AAV6 comprising the correctivedonor.

Briefly, human K562 cells were cultured in RPMI supplemented with 10%FBS and 200,000 cells were transfected with 400 ng DNA encoding each ofthe ZFNs by Amaxa Nucleofector® following the manufacturer'sinstructions. The cells were also treated with 1e6 vg/cell of the AAVdonor. Miseq next-generation sequencing analysis was used to detectZFN-induced modifications of the target gene (following cleavage). Inthis assay, PCR-amplification of the target site was followed by deepsequencing on the Illumina platform (“miSEQ”) was used according to themanufacturer's instructions to measure editing efficiency as well asnature of editing-generated alleles. The data is shown in FIG. 17, whereFIG. 17A depicts a drawing of the location of the primers used foramplifying maturely spliced RAG1 isoform 1 reverse-transcribed cDNAcontaining the exogenous transgene which had undergone targetedintegration into RAG1 intron 2. FIG. 17B shows the relative percentageof exogenous codon-optimized RAG1 cDNA in comparison to wild-type RAG1isoform 1 cDNA. FIG. 17C shows the amount of genome modification presentwithin these groups and demonstrates the targeted integration of thecorrective cDNA in the presence of ZFN and AAV6-donor.

The experiments were performed in CD34+ HSC/PC as well (FIG. 18) anddemonstrated that targeted integration of AAV6-delivered cDNA donorsoccurred using BTX electroporation of RAG1-specific ZFN pairs thattargeted both Site 1 (50698/50718) (FIG. 18A) and Site 4 (50773/49812)(FIG. 18B). RAG1-specific ZFNs were also electroporated at large scaleinto CD34+ HSC/PC (FIG. 19) using the Maxcyte device and weresubsequently shown to have targeted integration of AAV6-delivered cDNAdonors at both RAG1 intron 2 sites (FIG. 19B). Edited cells were alsotested for viability and found to be equally viable in the presence orabsence of the ZFNs and AAV6 donor (FIG. 19A).

Ex Vivo Methods

The genetically modified cells, particularly CD34+ HSPCs obtained fromX-SCID or Omenn Syndrome subjects (patient-derived CD34+ cells) aspreviously described (Aiuti et al. (2013) Science 341, 1233151),expressing IL2RG or RAG1 as described herein are administered to X-SCIDor Omenn Syndrome patients, respectively as previously described (Aiutiet al. ibid).

All patents, patent applications and publications mentioned herein arehereby incorporated by reference in their entirety.

Although disclosure has been provided in some detail by way ofillustration and example for the purposes of clarity of understanding,it will be apparent to those skilled in the art that various changes andmodifications can be practiced without departing from the spirit orscope of the disclosure. Accordingly, the foregoing descriptions andexamples should not be construed as limiting.

What is claimed is:
 1. A nuclease comprising a DNA-binding domain andcleavage domain, wherein the DNA-binding domain is a zinc finger protein(ZFP), a TAL-effector domain, or a single RNA (sgRNA) and furtherwherein the DNA-binding domain binds to a target site in intron 1 of anendogenous IL2RG gene or intron 1 or 2 of an endogenous RAG gene suchthat the nuclease cleaves the IL2RG or RAG gene.
 2. The nuclease ofclaim 1, wherein the DNA-binding domain comprises a zinc finger proteinthat binds to a sequence comprising a target site as shown in any of SEQID NOs:47-58 or 81-83.
 3. The nuclease of claim 2, wherein the zincfinger protein comprises recognition helix regions as shown in a singlerow of Table
 1. 4. The nuclease of claim 1, wherein the sgRNA comprisesa DNA-binding guide RNA as shown in Table
 5. 5. The nuclease of claim 1,wherein the TALE-effector domain comprises hypervariable diresidues(RVDs) as shown in in a single row of Table
 3. 6. A polynucleotideencoding a nuclease according to claim
 1. 7. A host cell comprising anexogenous sequence selected from the group consisting of: a sequenceencoding an IL2RG polypeptide integrated into intron 1 of an endogenousIL2RG gene; a sequence encoding a RAG polypeptide integrated into intron1 or 2 of an endogenous RAG gene; and combinations thereof, wherein theexogenous sequence is integrated into the host cell using a nucleaseaccording to claim
 1. 8. The host cell of claim 7, wherein the exogenoussequence comprises a cDNA selected from the group consisting of asequence comprising exons 2 through 8 of a wild type IL2RG gene; asequence comprising a full-length IL2RG gene; a sequence comprising exon3 of a wild type RAG gene and a sequence comprising a full-length RAGgene.
 9. The host cell of claim 7, wherein the cell is a hematopoieticstem cell or an induced pluripotent stem cell (iPSC).
 10. A method forcleaving an endogenous SCID-related gene in a cell, the methodcomprising: introducing, into the cell, one or more polynucleotidesaccording to claim 6 to the cell such that the nuclease(s) is(are)expressed and the one or more SCID-related genes are cleaved.
 11. Amethod for targeted integration of a gene encoding a protein lacking ordeficient in a subject with SCID, the method comprising: cleaving anendogenous SCID-related gene in a cell according to the method of claim10 in the presence of a donor sequence encoding at least a functionalfragment of the protein lacking or deficient in the subject with SCIDsuch that the donor sequence is integrated into the endogenousSCID-related gene.
 12. The method of claim 11, wherein the donorcomprises a cDNA selected from the group consisting of a sequencecomprising exons 2 through 8 of a wild type IL2RG gene; a sequencecomprising a full-length IL2RG gene; a sequence comprising exon 3 of awild type RAG gene and a sequence comprising a full-length RAG gene. 13.The method of claim 11, wherein the donor is carried on a viral ornon-viral vector.
 14. The method of claim 13, wherein the viral vectoris an adeno-associated vector (AAV).
 15. The method of claim 11, whereinthe gene lacking or deficient in the subject with SCID is expressedunder control of endogenous genetic control elements.
 16. The method ofclaim 11, wherein the donor sequence comprises an exogenous promoterthat drives expression of the gene lacking or deficient in the subjectwith a SCID.
 17. A method of treating or preventing SCID in a subject,the method comprising administering a host cell according to claim 7 tothe subject.
 18. A kit comprising a polynucleotide according to claim 6.19. A kit comprising a host cell according to claim 7.